1
|
Kaput J, Monteiro JP. Human Nutrition Research in the Data Era: Results of 11 Reports on the Effects of a Multiple-Micronutrient-Intervention Study. Nutrients 2024; 16:188. [PMID: 38257081 PMCID: PMC10819666 DOI: 10.3390/nu16020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Large datasets have been used in molecular and genetic research for decades, but only a few studies have included nutrition and lifestyle factors. Our team conducted an n-of-1 intervention with 12 vitamins and five minerals in 9- to 13-year-old Brazilian children and teens with poor healthy-eating indices. A unique feature of the experimental design was the inclusion of a replication arm. Twenty-six types of data were acquired including clinical measures, whole-genome mapping, whole-exome sequencing, and proteomic and a variety of metabolomic measurements over two years. A goal of this study was to use these diverse data sets to discover previously undetected physiological effects associated with a poor diet that include a more complete micronutrient composition. We summarize the key findings of 11 reports from this study that (i) found that LDL and total cholesterol and fasting glucose decreased in the population after the intervention but with inter-individual variation; (ii) associated a polygenic risk score that predicted baseline vitamin B12 levels; (iii) identified metabotypes linking diet intake, genetic makeup, and metabolic physiology; (iv) found multiple biomarkers for nutrient and food groups; and (v) discovered metabolites and proteins that are associated with DNA damage. This summary also highlights the limitations and lessons in analyzing diverse omic data.
Collapse
Affiliation(s)
| | - Jacqueline Pontes Monteiro
- Faculty of Medicine of Ribeirão Preto, Department of Pediatrics, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil;
| |
Collapse
|
2
|
Monteiro JP, Morine MJ, Ued FV, Kaput J. Identifying and Analyzing Topic Clusters in a Nutri-, Food-, and Diet-Proteomic Corpus Using Machine Reading. Nutrients 2023; 15:nu15020270. [PMID: 36678141 PMCID: PMC9863309 DOI: 10.3390/nu15020270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Nutrition affects the early stages of disease development, but the mechanisms remain poorly understood. High-throughput proteomic methods are being used to generate data and information on the effects of nutrients, foods, and diets on health and disease processes. In this report, a novel machine reading pipeline was used to identify all articles and abstracts on proteomics, diet, food, and nutrition in humans. The resulting proteomic corpus was further analyzed to produce seven clusters of "thematic" content defined as documents that have similar word content. Examples of publications from several of these clusters were then described in a similar way to a typical descriptive review.
Collapse
Affiliation(s)
- Jacqueline Pontes Monteiro
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil
- Correspondence:
| | | | - Fabio V. Ued
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil
| | | |
Collapse
|
3
|
|
4
|
de Barros TT, Venancio VDP, Hernandes LC, Antunes LMG, Hillesheim E, Salomão RG, Mathias MG, Coelho-Landell CA, Toffano RBD, Almada MORDV, Camelo-Junior JS, Moco S, Cominetti O, Ued FDV, Kaput J, Monteiro JP. DNA Damage, n-3 Long-Chain PUFA Levels and Proteomic Profile in Brazilian Children and Adolescents. Nutrients 2021; 13:nu13082483. [PMID: 34444642 PMCID: PMC8401971 DOI: 10.3390/nu13082483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 12/24/2022] Open
Abstract
Fatty acids play a significant role in maintaining cellular and DNA protection and we previously found an inverse relationship between blood levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and DNA damage. The aim of this study was to explore differences in proteomic profiles, for 117 pro-inflammatory proteins, in two previously defined groups of individuals with different DNA damage and EPA and DHA levels. Healthy children and adolescents (n = 140) aged 9 to 13 years old in an urban area of Brazil were divided by k-means cluster test into two clusters of DNA damage (tail intensity) using the comet assay (cluster 1 = 5.9% ± 1.2 and cluster 2 = 13.8% ± 3.1) in our previous study. The cluster with higher DNA damage and lower levels of DHA (6.2 ± 1.6 mg/dL; 5.4 ± 1.3 mg/dL, p = 0.003) and EPA (0.6 ± 0.2 mg/dL; 0.5 ± 0.1 mg/dL, p < 0.001) presented increased expression of the proteins CDK8-CCNC, PIK3CA-PIK3R1, KYNU, and PRKCB, which are involved in pro-inflammatory pathways. Our findings support the hypothesis that low levels of n-3 long-chain PUFA may have a less protective role against DNA damage through expression of pro-inflammatory proteins, such as CDK8-CCNC, PIK3CA-PIK3R1, KYNU, and PRKCB.
Collapse
Affiliation(s)
- Tamiris Trevisan de Barros
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
- Correspondence:
| | - Vinicius de Paula Venancio
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (V.d.P.V.); (L.M.G.A.)
| | - Lívia Cristina Hernandes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (V.d.P.V.); (L.M.G.A.)
| | - Lusania Maria Greggi Antunes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (V.d.P.V.); (L.M.G.A.)
| | - Elaine Hillesheim
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - Roberta Garcia Salomão
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - Mariana Giaretta Mathias
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - Carolina Almeida Coelho-Landell
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - Roseli Borges Donegá Toffano
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - Maria Olimpia Ribeiro do Vale Almada
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - José Simon Camelo-Junior
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| | - Sofia Moco
- Nestlé Research, Société des Produits Nestlé SA, EPFL Innovation Park, CH1015 Lausanne, Switzerland; (S.M.); (O.C.); (J.K.)
| | - Ornella Cominetti
- Nestlé Research, Société des Produits Nestlé SA, EPFL Innovation Park, CH1015 Lausanne, Switzerland; (S.M.); (O.C.); (J.K.)
| | - Fábio da Veiga Ued
- Department of Health Sciences, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil;
| | - Jim Kaput
- Nestlé Research, Société des Produits Nestlé SA, EPFL Innovation Park, CH1015 Lausanne, Switzerland; (S.M.); (O.C.); (J.K.)
| | - Jacqueline Pontes Monteiro
- Department of Pediatrics, Medical School of Ribeirao Preto, University of Sao Paulo, Sao Paulo 14049-900, Brazil; (E.H.); (R.G.S.); (M.G.M.); (C.A.C.-L.); (R.B.D.T.); (M.O.R.d.V.A.); (J.S.C.-J.); (J.P.M.)
| |
Collapse
|
5
|
Fuzo CA, da Veiga Ued F, Moco S, Cominetti O, Métairon S, Pruvost S, Charpagne A, Carayol J, Torrieri R, Silva WA, Descombes P, Kaput J, Monteiro JP. Contribution of genetic ancestry and polygenic risk score in meeting vitamin B12 needs in healthy Brazilian children and adolescents. Sci Rep 2021; 11:11992. [PMID: 34099811 PMCID: PMC8184816 DOI: 10.1038/s41598-021-91530-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/25/2021] [Indexed: 02/08/2023] Open
Abstract
Polymorphisms in genes related to the metabolism of vitamin B12 haven’t been examined in a Brazilian population.
To (a) determine the correlation between the local genetic ancestry components and vitamin B12 levels using ninety B12-related genes; (b) determine associations between these genes and their SNPs with vitamin B12 levels; (c) determine a polygenic risk score (PRS) using significant variants. This cross-sectional study included 168 children and adolescents, aged 9–13 years old. Total cobalamin was measured in plasma. Genotyping arrays and whole exome data were combined to yield ~ 7000 SNPs in 90 genes related to vitamin B12. The Efficient Local Ancestry Inference was used to estimate local ancestry for African (AFR), Native American, and European (EUR). The association between the genotypes and vitamin B12 levels were determined with generalized estimating equation.
Vitamin B12 levels were driven by positive (EUR) and negative (AFR, AMR) correlations with genetic ancestry. A set of 36 variants were used to create a PRS that explained 42% of vitamin level variation.
Vitamin B12 levels are influenced by genetic ancestry and a PRS explained almost 50% of the variation in plasma cobalamin in Brazilian children and adolescents.
Collapse
Affiliation(s)
- Carlos Alessandro Fuzo
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutics Sciences, University of São Paulo, Ribeirão Preto, Brazil
| | - Fábio da Veiga Ued
- Department of Pediatrics and Department of Health Sciences, Ribeirão Preto Medical School, Nutrition and Metabolism Section, University of São Paulo, Avenida Bandeirantes, 3900, Bairro Monte Alegre, Ribeirão Preto, SP, 14040-900, Brazil
| | - Sofia Moco
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteite Amsterdam, Amsterdam, The Netherlands
| | - Ornella Cominetti
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Sylviane Métairon
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Solenn Pruvost
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Aline Charpagne
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland.,Sophia Genetics, Campus Biotech, 1202, Geneva, Switzerland
| | - Jerome Carayol
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Raul Torrieri
- Center for Medical Genomics, Ribeirão Preto Medical School Hospital, University of São Paulo, Ribeirão Preto, Brazil
| | - Wilson Araujo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Patrick Descombes
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Jim Kaput
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland.,, Vydiant, Folsom, CA, USA
| | - Jacqueline Pontes Monteiro
- Department of Pediatrics and Department of Health Sciences, Ribeirão Preto Medical School, Nutrition and Metabolism Section, University of São Paulo, Avenida Bandeirantes, 3900, Bairro Monte Alegre, Ribeirão Preto, SP, 14040-900, Brazil.
| |
Collapse
|
6
|
de Barros TT, Venâncio VDP, Hernandes LC, Greggi Antunes LM, Hillesheim E, Salomão RG, Mathias MG, Coelho-Landell CA, Toffano RBD, Almada MORDV, Camelo- JS, Moco S, Ued FDV, Kaput J, Monteiro JP. DNA damage is inversely associated to blood levels of DHA and EPA fatty acids in Brazilian children and adolescents. Food Funct 2021; 11:5115-5121. [PMID: 32432238 DOI: 10.1039/c9fo02551k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This study aimed to investigate the association between DNA damage and blood levels of docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), retinol, beta-carotene and riboflavin in Brazilian children and adolescents. Subjects (n = 140) were healthy boys and girls aged 9 to 13 years in Ribeirão Preto (SP, Brazil). Data collection included anthropometry, assessment of energy intake and blood sampling. DNA damage was evaluated by single-cell gel electrophoresis (comet assay). Principal component analysis (PCA) was used to verify associations between blood concentrations of vitamins, polyunsaturated fatty acids and DNA damage. Multiple regression analyses, k-means cluster, and analysis of covariance (ANCOVA), adjusted for confounding variables such as age, sex, energy intake, body mass index and total cholesterol (when needed), were applied to confirm the associations. PCA explained 69.4% of the inverse relationships between DNA damage and blood levels of DHA, EPA, retinol, and beta-carotene. Results were confirmed by ANCOVA and multiple regression analyses for DHA and EPA. In conclusion, omega-3-fatty acids were inversely associated with DNA damage in Brazilian children and adolescents and may be a protective factor against the development of future diseases.
Collapse
Affiliation(s)
- Tamiris Trevisan de Barros
- Department of Pediatrics and Department of Health Sciences, Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Vinicius de Paula Venâncio
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Lívia Cristina Hernandes
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Elaine Hillesheim
- Department of Pediatrics and Department of Health Sciences, Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Roberta Garcia Salomão
- Department of Pediatrics and Department of Health Sciences, Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Mariana Giaretta Mathias
- Department of Pediatrics and Department of Health Sciences, Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Carolina Almeida Coelho-Landell
- Department of Pediatrics and Department of Health Sciences, Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Roseli Borges Donegá Toffano
- Department of Pediatrics and Department of Health Sciences, Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Maria Olimpia Ribeiro do Vale Almada
- Department of Pediatrics and Department of Health Sciences, Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - José Simon Camelo-
- Department of Pediatrics and Department of Health Sciences, Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Sofia Moco
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Fábio da Veiga Ued
- Department of Pediatrics and Department of Health Sciences, Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Jim Kaput
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Jacqueline Pontes Monteiro
- Department of Pediatrics and Department of Health Sciences, Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| |
Collapse
|
7
|
Almada MORDV, Almeida ACF, Ued FDV, Mathias MG, Coelho-Landell CDA, SalomÃo RG, Toffano RBD, Camarneiro JM, Hillesheim E, Barros TTD, Camelo-Junior JS, Moco S, Kaput J, Monteiro JP. Metabolic Groups Related to Blood Vitamin Levels and Inflammatory Biomarkers in Brazilian Children and Adolescents. J Nutr Sci Vitaminol (Tokyo) 2021; 66:515-525. [PMID: 33390393 DOI: 10.3177/jnsv.66.515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Certain B-vitamins and vitamin A may be involved in inflammatory pathways associated with homocysteine and omega-3 fatty acids. The aims of this study were (i) to determine whether different metabolic profiles of B-vitamins and vitamin A in Brazilian children and adolescents were positively or negatively related to homocysteine and omega-3 fatty acids using k-means clustering analysis, (ii) compare nutrient intakes and metabolites between the different metabolic profiles, (iii) evaluate if the statistically significant metabolites found between the metabolic groups, can predict the variation of leukotriene A4 hydrolase (LTA4H) levels, a biomarker of low-grade inflammation, in the total studied population. This cross-sectional study included 124 children and adolescents, aged 9-13 y old. Dietary intake was assessed by the food frequency questionnaire and 24-hour recall. Biomarkers for vitamins B2, B6, B12, folate and vitamin A were measured in plasma. Omega-3 fatty acids and homocysteine were measured in red blood cells (RBC). Two different metabolic profiles were found. Thirty of these individuals had overall average higher riboflavin, pyridoxal, and vitamin B12 plasma levels (metabolic group 1) compared to 94 individuals (group 2). Group 2 had lower dietary intake of vitamin B2, vitamin A, and vitamin B12 and higher RBC levels of homocysteine. EPA and DHA erythrocyte levels were not different between metabolic groups. Multiple linear regression analyses showed that blood cobalamin, riboflavin, pyridoxal and homocysteine combined, explained 9.0% of LTA4H levels variation in the total studied population. The metabolic group that had low plasma levels of riboflavin, pyridoxal, and cobalamin also had a lower dietary intake of B-vitamin and higher RBC homocysteine. The combined levels of the riboflavin, pyridoxal, cobalamin and homocysteine biomarkers can predict the variation of LTA4H in the total population studied, but it is not clear how this regulation occurs.
Collapse
Affiliation(s)
| | | | - Fábio da Veiga Ued
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo.,Department of Health Sciences, Ribeirão Preto Medical School, University of São Paulo
| | | | | | | | | | | | - Elaine Hillesheim
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo
| | | | | | - Sofia Moco
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne
| | - Jim Kaput
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale de Lausanne
| | - Jacqueline Pontes Monteiro
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo.,Department of Health Sciences, Ribeirão Preto Medical School, University of São Paulo
| |
Collapse
|
8
|
Tini G, Varma V, Lombardo R, Nolen GT, Lefebvre G, Descombes P, Métairon S, Priami C, Kaput J, Scott-Boyer MP. DNA methylation during human adipogenesis and the impact of fructose. Genes Nutr 2020; 15:21. [PMID: 33243154 PMCID: PMC7691080 DOI: 10.1186/s12263-020-00680-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 11/10/2020] [Indexed: 01/12/2023]
Abstract
BACKGROUND Increased adipogenesis and altered adipocyte function contribute to the development of obesity and associated comorbidities. Fructose modified adipocyte metabolism compared to glucose, but the regulatory mechanisms and consequences for obesity are unknown. Genome-wide methylation and global transcriptomics in SGBS pre-adipocytes exposed to 0, 2.5, 5, and 10 mM fructose, added to a 5-mM glucose-containing medium, were analyzed at 0, 24, 48, 96, 192, and 384 h following the induction of adipogenesis. RESULTS Time-dependent changes in DNA methylation compared to baseline (0 h) occurred during the final maturation of adipocytes, between 192 and 384 h. Larger percentages (0.1% at 192 h, 3.2% at 384 h) of differentially methylated regions (DMRs) were found in adipocytes differentiated in the glucose-containing control media compared to adipocytes differentiated in fructose-supplemented media (0.0006% for 10 mM, 0.001% for 5 mM, and 0.005% for 2.5 mM at 384 h). A total of 1437 DMRs were identified in 5237 differentially expressed genes at 384 h post-induction in glucose-containing (5 mM) control media. The majority of them inversely correlated with the gene expression, but 666 regions were positively correlated to the gene expression. CONCLUSIONS Our studies demonstrate that DNA methylation regulates or marks the transformation of morphologically differentiating adipocytes (seen at 192 h), to the more mature and metabolically robust adipocytes (as seen at 384 h) in a genome-wide manner. Lower (2.5 mM) concentrations of fructose have the most robust effects on methylation compared to higher concentrations (5 and 10 mM), suggesting that fructose may be playing a signaling/regulatory role at lower concentrations of fructose and as a substrate at higher concentrations.
Collapse
Affiliation(s)
- Giulia Tini
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, 38068, Rovereto, Italy.,Department of Mathematics, University of Trento, Via Sommarive 14, 38050, Povo, Italy.,Present address: Department of Experimental Oncology, IEO European Institute of Oncology IRCSS, Milan, Italy
| | - Vijayalakshmi Varma
- Division of Systems Biology, National Center for Toxicological Research, FDA, 3900 NCTR Road, Jefferson, AR, 72079, USA.,Present Address: Cardiovascular Renal and Metabolism Division of MedImmune, Astrazeneca, Gaithersburg, MD, 20878, USA
| | - Rosario Lombardo
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, 38068, Rovereto, Italy
| | - Greg T Nolen
- Division of Systems Biology, National Center for Toxicological Research, FDA, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | | | | | | | - Corrado Priami
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, 38068, Rovereto, Italy.,Department of Computer Science, University of Pisa, Pisa, Italy
| | - Jim Kaput
- Nestlé Institute of Health Science, Lausanne, Switzerland.,Present Addresses: Vydiant Inc., Folsom, CA, 95630, USA
| | - Marie-Pier Scott-Boyer
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, 38068, Rovereto, Italy. .,Present Address: CRCHU de Québec-Université Laval, Quebec City, Québec, Canada.
| |
Collapse
|
9
|
Hillesheim E, Toffano RBD, Barros TTD, Salomão RG, Mathias MG, Coelho-Landell CDA, Almada MORDV, Camarneiro JM, Camelo-Junior JS, Ued FDV, Campos-Gimenez E, Redeuil K, Giner MP, Martin FP, Montoliu I, Moco S, Kaput J, Monteiro JP. Biomarker-based validity of a food frequency questionnaire estimating intake in Brazilian children and adolescents. Int J Food Sci Nutr 2020; 72:236-247. [PMID: 32631124 DOI: 10.1080/09637486.2020.1786026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This study evaluated the validity of nutrient and food group intakes estimated by an FFQ against biomarkers. A 71-item semiquantitative FFQ was administered to 210 Brazilian children and adolescents aged 9-13 years. Intakes were correlated with biomarkers in plasma and red blood cells. Correlations between nutrients and their biomarkers were presented for animal protein, myristic acid (C14:0), EPA, DHA, β-carotene, folate, and vitamins B3, B5 and B6. Food groups and biomarkers were correlated as follows: fish products with EPA and DHA; milk and dairy with C14:0, pyridoxal 5'-phosphate and vitamin B12; total vegetables and dark green and orange vegetables with β-carotene; 5-methyltetrahydrofolate with green vegetables; and flour products with para-aminobenzoylglutamic acid. This FFQ is a valid tool for ranking Brazilian children and adolescents according to their intake of several nutrients and food groups.
Collapse
Affiliation(s)
- Elaine Hillesheim
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Tamiris Trevisan de Barros
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Roberta Garcia Salomão
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Department of Health Sciences, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Mariana Giaretta Mathias
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | | | - Joyce Moraes Camarneiro
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - José Simon Camelo-Junior
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Fábio da Veiga Ued
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Department of Health Sciences, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | | | | | | | - Ivan Montoliu
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Sofia Moco
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Jim Kaput
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Jacqueline Pontes Monteiro
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Department of Health Sciences, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| |
Collapse
|
10
|
|
11
|
Coelho‐Landell CA, Salomão RG, Almada MORDV, Mathias MG, Toffano RBD, Hillesheim E, Barros TT, Camarneiro JM, Camelo‐Junior JS, Rosa JC, Izumi C, Czernisz É, Moco S, Kaput J, Monteiro JP. Metabo groups in response to micronutrient intervention: Pilot study. Food Sci Nutr 2020; 8:683-693. [PMID: 31993192 PMCID: PMC6977437 DOI: 10.1002/fsn3.1357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/22/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022] Open
Abstract
Micronutrients and their metabolites are cofactors in proteins involved in lipid metabolism. The present study was a subproject of the Harmonized Micronutrient Project (ClinTrials.gov # NCT01823744). Twenty participants were randomly selected from 136 children and adolescents that consumed a daily dose of 12 vitamins and 5 minerals supplementation for 6 weeks. The 20 individuals were divided into two pools of 10 individuals, according to their lipid profile at baseline (Pool 1 with lower triglycerides, LDL, and VLDL). The individuals were analyzed at baseline, after 6 weeks of daily supplementation, and after 6 weeks of a washout period in relation to anthropometric, body composition, food intake, lipid profile, micronutrient levels, and iTRAQ proteomic data. Genetic ancestry and its association with vitamin serum levels were also determined. After supplementation, LDL levels decreased while alpha-tocopherol and pantothenic acid levels increased in pool 2; lipid profiles in pool 1 did not change but had higher plasma levels of pantothenic acid, pyridoxal, and pyridoxic acid. In pool 2, expression of some proteins increased, and expression of other ones decreased after intervention, while in pool 1, the same proteins responded inversely or did not change their levels. Plasma alpha-tocopherol and Native American genetic ancestry explained a significant fraction of LDL plasma levels at baseline and in response to the intervention. After intervention, changes in expression of alpha-1 antitrypsin, haptoglobin, Ig alpha-1 chain C region, plasma protease C1 inhibitor, alpha-1-acid glycoprotein 1, fibrinogen alpha, beta, and gamma-chain in individuals in pool 2 may be associated with levels of LDL and vitamin E. Vitamin E and Native American genetic ancestry may also be implicated in changes of vitamin E and LDL levels. The results of this pilot study must be validated in future studies with larger sample size or in in vitro studies.
Collapse
Affiliation(s)
- Carolina Almeida Coelho‐Landell
- Department of Pediatrics and Department of Health SciencesFaculty of Medicine of Ribeirão PretoUniversity of São PauloSão PauloBrazil
| | - Roberta Garcia Salomão
- Department of Pediatrics and Department of Health SciencesFaculty of Medicine of Ribeirão PretoUniversity of São PauloSão PauloBrazil
| | | | - Mariana Giaretta Mathias
- Department of Pediatrics and Department of Health SciencesFaculty of Medicine of Ribeirão PretoUniversity of São PauloSão PauloBrazil
| | - Roseli Borges Donega Toffano
- Department of Pediatrics and Department of Health SciencesFaculty of Medicine of Ribeirão PretoUniversity of São PauloSão PauloBrazil
| | - Elaine Hillesheim
- Department of Pediatrics and Department of Health SciencesFaculty of Medicine of Ribeirão PretoUniversity of São PauloSão PauloBrazil
| | - Tamiris Trevisan Barros
- Department of Pediatrics and Department of Health SciencesFaculty of Medicine of Ribeirão PretoUniversity of São PauloSão PauloBrazil
| | - Joyce Moraes Camarneiro
- Department of Pediatrics and Department of Health SciencesFaculty of Medicine of Ribeirão PretoUniversity of São PauloSão PauloBrazil
| | - José Simon Camelo‐Junior
- Department of Pediatrics and Department of Health SciencesFaculty of Medicine of Ribeirão PretoUniversity of São PauloSão PauloBrazil
| | - José Cesar Rosa
- Department of Molecular and Cell Biology and Pathogenic BioagentsProtein Chemistry CenterMedical School of Ribeirão PretoUniversity of São PauloRibeirão PretoBrazil
| | - Clarice Izumi
- Department of Molecular and Cell Biology and Pathogenic BioagentsProtein Chemistry CenterMedical School of Ribeirão PretoUniversity of São PauloRibeirão PretoBrazil
| | - Érika Czernisz
- Department of Molecular and Cell Biology and Pathogenic BioagentsProtein Chemistry CenterMedical School of Ribeirão PretoUniversity of São PauloRibeirão PretoBrazil
| | - Sofia Moco
- Nestlé Institute of Health SciencesNestle ResearchEPFL Innovation ParkLausanneSwitzerland
| | - Jim Kaput
- Nestlé Institute of Health SciencesNestle ResearchEPFL Innovation ParkLausanneSwitzerland
- Present address:
VydiantSacramentoCAUSA
| | - Jacqueline Pontes Monteiro
- Department of Pediatrics and Department of Health SciencesFaculty of Medicine of Ribeirão PretoUniversity of São PauloSão PauloBrazil
| |
Collapse
|
12
|
de Roos B, Aura AM, Bronze M, Cassidy A, Conesa MTG, Gibney ER, Greyling A, Kaput J, Kerem Z, Knežević N, Kroon P, Landberg R, Manach C, Milenkovic D, Rodriguez-Mateos A, Tomás-Barberán FA, van de Wiele T, Morand C. Targeting the delivery of dietary plant bioactives to those who would benefit most: from science to practical applications. Eur J Nutr 2019; 58:65-73. [PMID: 31637468 PMCID: PMC6851046 DOI: 10.1007/s00394-019-02075-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/02/2019] [Indexed: 03/19/2023]
Abstract
Background A healthy diet and optimal lifestyle choices are amongst the most important actions for the prevention of cardiometabolic diseases. Despite this, it appears difficult to convince consumers to select more nutritious foods. Furthermore, the development and production of healthier foods do not always lead to economic profits for the agro-food sector. Most dietary recommendations for the general population represent a “one-size-fits-all approach” which does not necessarily ensure that everyone has adequate exposure to health-promoting constituents of foods. Indeed, we now know that individuals show a high variability in responses when exposed to specific nutrients, foods, or diets. Purpose This review aims to highlight our current understanding of inter-individual variability in response to dietary bioactives, based on the integration of findings of the COST Action POSITIVe. We also evaluate opportunities for translation of scientific knowledge on inter-individual variability in response to dietary bioactives, once it becomes available, into practical applications for stakeholders, such as the agro-food industry. The potential impact from such applications will form an important impetus for the food industry to develop and market new high quality and healthy foods for specific groups of consumers in the future. This may contribute to a decrease in the burden of diet-related chronic diseases. Individual differences in ADME (Absorption, Digestion, Metabolism and Excretion) is believed to underpin much of the inter-individual variation in responses. Recent developments in the area of food metabolome databases and fast improvements in innovative metabotyping technologies hold great promise for improved profiling of dietary intake, exposure to individual ingredients, foods and dietary patterns, as well as our ability to identify individual responsiveness. The food industry needs well-defined population clusters or targets in order to be able to design “personalized products”. There are indeed excellent industrial opportunities for foods that modulate gut microbiota, and thereby enable the delivery of food bioactive metabolites. It is currently not clear whether knowledge on individual nutrient needs, based on genetic or metagenomic data, would affect long-term dietary and health behaviours. Data to support the development of dietary recommendations may need to be generated by new n-of-1-based study designs in the future.
Collapse
Affiliation(s)
- Baukje de Roos
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
| | - Anna-Marja Aura
- VTT Technical Research Centre of Finland, PO Box 1000, Tietotie 2, Espoo, Finland
| | - Maria Bronze
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, Portugal
| | - Aedin Cassidy
- Department of Nutrition and Preventive Medicine, Norwich Medical School, University of East Anglia, Norwich, UK
| | - María-Teresa Garcia Conesa
- Food and Health Laboratory. Research Group on Quality, Safety, and Bioactivity of Plant Foods, CEBAS-CSIC, Campus de Espinardo, Murcia, Spain
| | - Eileen R Gibney
- UCD Institute of Food and Health, School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Arno Greyling
- Unilever Research and Development Vlaardingen, Vlaardingen, The Netherlands
| | | | - Zohar Kerem
- R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Paul Kroon
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Claudine Manach
- INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Dragan Milenkovic
- INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ana Rodriguez-Mateos
- Department of Nutritional Sciences, Faculty of Life Sciences and Medicine, School of Life Course Sciences, King's College London, London, UK
| | - Francisco A Tomás-Barberán
- Food and Health Laboratory. Research Group on Quality, Safety, and Bioactivity of Plant Foods, CEBAS-CSIC, Campus de Espinardo, Murcia, Spain
| | - Tom van de Wiele
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Christine Morand
- INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| |
Collapse
|
13
|
Chakrabarti A, Eiden M, Morin-Rivron D, Christinat N, Monteiro JP, Kaput J, Masoodi M. Impact of multi-micronutrient supplementation on lipidemia of children and adolescents. Clin Nutr 2019; 39:2211-2219. [PMID: 31677804 DOI: 10.1016/j.clnu.2019.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Micronutrient supplementation has been extensively explored as a strategy to improve health and reduce risk of chronic diseases. Fat-soluble vitamins like A and E with their antioxidant properties and mechanistic interactions with lipoproteins, have potentially a key impact on lipid metabolism and lipidemia. OBJECTIVE The impact of micronutrients on lipid metabolism requires further investigation including characterization of plasma lipidome following supplementation and any cause-effect on circulating lipids. DESIGN In this study, we elucidate the effect and associations of a multi-micronutrient intervention in Brazilian children and teens with lipoprotein alterations and lipid metabolism. RESULTS Our analysis suggests a combination of short and long-term impact of supplementation on lipid metabolism, potentially mediated primarily by α-tocopherol (vitamin E) and retinol (vitamin A). Among the lipid classes, levels of phospholipids, lysophospholipids, and cholesterol esters were impacted the most along with differential incorporation of stearic, palmitic, oleic and arachidonic acids. Integrated analysis with proteomic data suggested potential links to supplementation-mediated alterations in protein levels of phospholipases and pyruvate dehydrogenase kinase 1 (PDK1). CONCLUSIONS Associations between the observed differences in lipidemia, total triglyceride, and VLDL-cholesterol levels suggest that micronutrients may play a role in reducing these risk factors for cardiovascular disease in children. This would require further investigation.
Collapse
Affiliation(s)
| | - Michael Eiden
- Lipid Metabolism, Nestlé Research, EPFL Innovation Park, 1015, Switzerland; Eidea Bioscience Ltd., Cambridge, United Kingdom
| | | | - Nicolas Christinat
- Lipid Metabolism, Nestlé Research, EPFL Innovation Park, 1015, Switzerland
| | - Jacqueline P Monteiro
- Department of Pediatrics and Department of Health Sciences, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Jim Kaput
- Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Mojgan Masoodi
- Lipid Metabolism, Nestlé Research, EPFL Innovation Park, 1015, Switzerland; Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland.
| |
Collapse
|
14
|
Curran AM, Scott-Boyer MP, Kaput J, Ryan MF, Drummond E, Gibney ER, Gibney MJ, Roche HM, Brennan L. A proteomic signature that reflects pancreatic beta-cell function. PLoS One 2018; 13:e0202727. [PMID: 30161145 PMCID: PMC6117012 DOI: 10.1371/journal.pone.0202727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/08/2018] [Indexed: 01/08/2023] Open
Abstract
AIM Proteomics has the potential to enhance early identification of beta-cell dysfunction, in conjunction with monitoring the various stages of type 2 diabetes onset. The most routine method of assessing pancreatic beta-cell function is an oral glucose tolerance test, however this method is time consuming and carries a participant burden. The objectives of this research were to identify protein signatures and pathways related to pancreatic beta-cell function in fasting blood samples. METHODS Beta-cell function measures were calculated for MECHE study participants who completed an oral glucose tolerance test and had proteomic data (n = 100). Information on 1,129 protein levels was obtained using the SOMAscan assay. Receiver operating characteristic curves were used to assess discriminatory ability of proteins of interest. Subsequent in vitro experiments were performed using the BRIN-BD11 pancreatic beta-cell line. Replication of findings were achieved in a second human cohort where possible. RESULTS Twenty-two proteins measured by aptamer technology were significantly associated with beta-cell function/HOMA-IR while 17 proteins were significantly associated with the disposition index (p ≤ 0.01). Receiver operator characteristic curves determined the protein panels to have excellent discrimination between low and high beta-cell function. Linear regression analysis determined that beta-endorphin and IL-17F have strong associations with beta-cell function/HOMA-IR, β = 0.039 (p = 0.005) and β = -0.027 (p = 0.013) respectively. Calcineurin and CRTAM were strongly associated with the disposition index (β = 0.005 and β = 0.005 respectively, p = 0.012). In vitro experiments confirmed that IL-17F modulated insulin secretion in the BRIN-BD11 cell line, with the lower concentration of 10 ng/mL significantly increasing glucose stimulated insulin secretion (p = 0.043). CONCLUSIONS Early detection of compromised beta-cell function could allow for implementation of nutritional and lifestyle interventions before progression to type 2 diabetes.
Collapse
Affiliation(s)
- Aoife M. Curran
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Food for Health Ireland (FHI), University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
| | - Marie Pier Scott-Boyer
- The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Jim Kaput
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Miriam F. Ryan
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
| | - Elaine Drummond
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Food for Health Ireland (FHI), University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
| | - Eileen R. Gibney
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Food for Health Ireland (FHI), University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
| | - Michael J. Gibney
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Food for Health Ireland (FHI), University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
| | - Helen M. Roche
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Food for Health Ireland (FHI), University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Nutrigenomics Research Group, UCD Conway Institute of Biomolecular and Biomedical Research and UCD Institute of Food and Health, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin, Republic of Ireland
| | - Lorraine Brennan
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Food for Health Ireland (FHI), University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- * E-mail:
| |
Collapse
|
15
|
Mathias MG, Coelho‐Landell CDA, Scott‐Boyer M, Lacroix S, Morine MJ, Salomão RG, Toffano RBD, Almada MORDV, Camarneiro JM, Hillesheim E, de Barros TT, Camelo‐Junior JS, Campos Giménez E, Redeuil K, Goyon A, Bertschy E, Lévêques A, Oberson J, Giménez C, Carayol J, Kussmann M, Descombes P, Métairon S, Draper CF, Conus N, Mottaz SC, Corsini GZ, Myoshi SKB, Muniz MM, Hernandes LC, Venâncio VP, Antunes LMG, da Silva RQ, Laurito TF, Rossi IR, Ricci R, Jorge JR, Fagá ML, Quinhoneiro DCG, Reche MC, Silva PVS, Falquetti LL, da Cunha THA, Deminice TMM, Tambellini TH, de Souza GCA, de Oliveira MM, Nogueira‐Pileggi V, Matsumoto MT, Priami C, Kaput J, Monteiro JP. Clinical and Vitamin Response to a Short-Term Multi-Micronutrient Intervention in Brazilian Children and Teens: From Population Data to Interindividual Responses. Mol Nutr Food Res 2018; 62:e1700613. [PMID: 29368422 PMCID: PMC6120145 DOI: 10.1002/mnfr.201700613] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/02/2017] [Indexed: 12/11/2022]
Abstract
SCOPE Micronutrients are in small amounts in foods, act in concert, and require variable amounts of time to see changes in health and risk for disease. These first principles are incorporated into an intervention study designed to develop new experimental strategies for setting target recommendations for food bioactives for populations and individuals. METHODS AND RESULTS A 6-week multivitamin/mineral intervention is conducted in 9-13 year olds. Participants (136) are (i) their own control (n-of-1); (ii) monitored for compliance; (iii) measured for 36 circulating vitamin forms, 30 clinical, anthropometric, and food intake parameters at baseline, post intervention, and following a 6-week washout; and (iv) had their ancestry accounted for as modifier of vitamin baseline or response. The same intervention is repeated the following year (135 participants). Most vitamins respond positively and many clinical parameters change in directions consistent with improved metabolic health to the intervention. Baseline levels of any metabolite predict its own response to the intervention. Elastic net penalized regression models are identified, and significantly predict response to intervention on the basis of multiple vitamin/clinical baseline measures. CONCLUSIONS The study design, computational methods, and results are a step toward developing recommendations for optimizing vitamin levels and health parameters for individuals.
Collapse
Affiliation(s)
| | | | - Marie‐Pier Scott‐Boyer
- The Microsoft Research, Centre for Computational and Systems Biology (COSBI)University of TrentoRoveretoItaly
| | - Sébastien Lacroix
- The Microsoft Research, Centre for Computational and Systems Biology (COSBI)University of TrentoRoveretoItaly
| | - Melissa J. Morine
- The Microsoft Research, Centre for Computational and Systems Biology (COSBI)University of TrentoRoveretoItaly
- Department of MathematicsUniversity of TrentoTrentoItaly
| | - Roberta Garcia Salomão
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | | | | | - Elaine Hillesheim
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Nelly Conus
- Nestlé Institute of Health SciencesLausanneSwitzerland
| | | | | | | | - Mariana Mendes Muniz
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | - Vinícius Paula Venâncio
- School of Pharmaceutical Science of Ribeirao PretoUniversity of São PauloRibeirao PretoBrazil
| | | | | | - Taís Fontellas Laurito
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | - Isabela Ribeiro Rossi
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | - Raquel Ricci
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | - Jéssica Ré Jorge
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | - Mayara Leite Fagá
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | | | | | - Letícia Lima Falquetti
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | | | | | | | | | - Vicky Nogueira‐Pileggi
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | - Corrado Priami
- The Microsoft Research, Centre for Computational and Systems Biology (COSBI)University of TrentoRoveretoItaly
- Department of MathematicsUniversity of TrentoTrentoItaly
| | - Jim Kaput
- Nestlé Institute of Health SciencesLausanneSwitzerland
| | | |
Collapse
|
16
|
Lacroix S, Klicic Badoux J, Scott-Boyer MP, Parolo S, Matone A, Priami C, Morine MJ, Kaput J, Moco S. A computationally driven analysis of the polyphenol-protein interactome. Sci Rep 2018; 8:2232. [PMID: 29396566 PMCID: PMC5797150 DOI: 10.1038/s41598-018-20625-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/22/2018] [Indexed: 01/08/2023] Open
Abstract
Polyphenol-rich foods are part of many nutritional interventions aimed at improving health and preventing cardiometabolic diseases (CMDs). Polyphenols have oxidative, inflammatory, and/or metabolic effects. Research into the chemistry and biology of polyphenol bioactives is prolific but knowledge of their molecular interactions with proteins is limited. We mined public data to (i) identify proteins that interact with or metabolize polyphenols, (ii) mapped these proteins to pathways and networks, and (iii) annotated functions enriched within the resulting polyphenol-protein interactome. A total of 1,395 polyphenols and their metabolites were retrieved (using Phenol-Explorer and Dictionary of Natural Products) of which 369 polyphenols interacted with 5,699 unique proteins in 11,987 interactions as annotated in STITCH, Pathway Commons, and BindingDB. Pathway enrichment analysis using the KEGG repository identified a broad coverage of significant pathways of low specificity to particular polyphenol (sub)classes. When compared to drugs or micronutrients, polyphenols have pleiotropic effects across many biological processes related to metabolism and CMDs. These systems-wide effects were also found in the protein interactome of the polyphenol-rich citrus fruits, used as a case study. In sum, these findings provide a knowledgebase for identifying polyphenol classes (and polyphenol-rich foods) that individually or in combination influence metabolism.
Collapse
Affiliation(s)
- Sébastien Lacroix
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
- Institute of Nutrition and Functional Foods (INAF), Québec, Canada
| | | | - Marie-Pier Scott-Boyer
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
- Centre de Recherche du Centre Hospitalier Universitaire de Québec (CRCHUQ), Québec, Canada
| | - Silvia Parolo
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Alice Matone
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Corrado Priami
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
- Department of Computer Science, University of Pisa, Pisa (PI), Italy
| | - Melissa J Morine
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Jim Kaput
- Nestle Institute of Health Sciences, Lausanne, Switzerland
| | - Sofia Moco
- Nestle Institute of Health Sciences, Lausanne, Switzerland.
| |
Collapse
|
17
|
Toffano RBD, Hillesheim E, Mathias MG, Coelho-Landell CA, Salomão RG, Almada MORV, Camarneiro JM, Barros TT, Camelo-Junior JS, Rezzi S, Goulet L, Giner MP, Silva LD, Martin FP, Montoliu I, Moco S, Collino S, Kaput J, Monteiro JP. Validation of the Brazilian Healthy Eating Index-Revised Using Biomarkers in Children and Adolescents. Nutrients 2018; 10:E154. [PMID: 29385742 PMCID: PMC5852730 DOI: 10.3390/nu10020154] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/26/2017] [Accepted: 01/08/2018] [Indexed: 12/22/2022] Open
Abstract
The Brazilian Healthy Eating Index-Revised (BHEI-R) can be used to determine overall dietary patterns. We assessed the BHEI-R scores in children and adolescents, aged from 9 to 13 years old, and associated its component scores with biomarkers of health and dietary exposure. Three 24-h recalls were used to generate BHEI-R. Biomarkers were analyzed in plasma and red blood cells. Correlation tests, agreement, and covariance analyses were used to associate BHEI-R components with biomarkers. Data from 167 subjects were used. The strongest correlations were between fruits, vegetables and legumes with omega-6 and omega-3 fatty acids, and β-carotene intakes. Milk and dairy correlated with plasma retinol and pyridoxine. All components rich in vegetable and animal protein sources correlated with plasma creatine. Total BHEI-R scores were positively associated with intakes of omega-6, omega-3, fiber and vitamin C, and inversely associated with energy and saturated fat intakes of individuals. Plasma β-carotene and riboflavin biomarkers were positively associated with total BHEI-R. An inadequate food consumption pattern was captured by both biomarkers of health and dietary exposure. BHEI-R was validated for the above dietary components and can be associated with metabolomics and nutritional epidemiological data in future pediatric studies.
Collapse
Affiliation(s)
- Roseli B D Toffano
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil.
| | - Elaine Hillesheim
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil.
| | - Mariana G Mathias
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil.
| | - Carolina A Coelho-Landell
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil.
| | - Roberta G Salomão
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil.
| | - Maria O R V Almada
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil.
| | - Joyce M Camarneiro
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil.
| | - Tamiris T Barros
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil.
| | - José S Camelo-Junior
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil.
| | - Serge Rezzi
- Nestlé Institute of Health Sciences, Innovation Square, École Polytechnique Fédérale de Lausanne, Campus, 1015 Lausanne, Switzerland.
| | - Laurence Goulet
- Nestlé Institute of Health Sciences, Innovation Square, École Polytechnique Fédérale de Lausanne, Campus, 1015 Lausanne, Switzerland.
| | - Maria P Giner
- Nestlé Institute of Health Sciences, Innovation Square, École Polytechnique Fédérale de Lausanne, Campus, 1015 Lausanne, Switzerland.
| | - Laeticia Da Silva
- Nestlé Institute of Health Sciences, Innovation Square, École Polytechnique Fédérale de Lausanne, Campus, 1015 Lausanne, Switzerland.
| | - Francois-Pierre Martin
- Nestlé Institute of Health Sciences, Innovation Square, École Polytechnique Fédérale de Lausanne, Campus, 1015 Lausanne, Switzerland.
| | - Ivan Montoliu
- Nestlé Institute of Health Sciences, Innovation Square, École Polytechnique Fédérale de Lausanne, Campus, 1015 Lausanne, Switzerland.
| | - Sofia Moco
- Nestlé Institute of Health Sciences, Innovation Square, École Polytechnique Fédérale de Lausanne, Campus, 1015 Lausanne, Switzerland.
| | - Sebastiano Collino
- Nestlé Institute of Health Sciences, Innovation Square, École Polytechnique Fédérale de Lausanne, Campus, 1015 Lausanne, Switzerland.
| | - Jim Kaput
- Nestlé Institute of Health Sciences, Innovation Square, École Polytechnique Fédérale de Lausanne, Campus, 1015 Lausanne, Switzerland.
| | - Jacqueline P Monteiro
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Bandeirantes Avenue, 3900, Ribeirão Preto 14049-900, Brazil.
| |
Collapse
|
18
|
Draper CF, Vassallo I, Di Cara A, Milone C, Comminetti O, Monnard I, Godin JP, Scherer M, Su M, Jia W, Guiraud SP, Praplan F, Guignard L, Ammon Zufferey C, Shevlyakova M, Emami N, Moco S, Beaumont M, Kaput J, Martin FP. A 48-Hour Vegan Diet Challenge in Healthy Women and Men Induces a BRANCH-Chain Amino Acid Related, Health Associated, Metabolic Signature. Mol Nutr Food Res 2017; 62. [PMID: 29087622 DOI: 10.1002/mnfr.201700703] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/24/2017] [Indexed: 12/14/2022]
Abstract
SCOPE Research is limited on diet challenges to improve health. A short-term, vegan protein diet regimen nutritionally balanced in macronutrient composition compared to an omnivorous diet is hypothesized to improve metabolic measurements of blood sugar regulation, blood lipids, and amino acid metabolism. METHODS AND RESULTS This randomized, cross-over, controlled vegan versus animal diet challenge is conducted on 21 (11 female,10 male) healthy participants. Fasting plasma is measured during a 3 d diet intervention for clinical biochemistry and metabonomics. Intervention diet plans meet individual caloric needs. Meals are provided and supervised. Diet compliance is monitored. CONCLUSIONS The vegan diet lowers triglycerides, insulin and homeostatic model assessment (HOMA-IR), bile acids, elevated magnesium levels, and changed branched-chain amino acids (BCAAs) metabolism (p < 0.05), potentiating insulin and blood sugar control after 48 h. Cholesterol control improves significantly in the vegan versus omnivorous diets. Plasma amino acid and magnesium concentrations positively correlate with dietary amino acids. Polyunsaturated fatty acids and dietary fiber inversely correlate with insulin, HOMA-IR, and triglycerides. Nutritional biochemistries, BCAAs, insulin, and HOMA-IR are impacted by sexual dimorphism. A health-promoting, BCAA-associated metabolic signature is produced from a short-term, healthy, controlled, vegan diet challenge when compared with a healthy, controlled, omnivorous diet.
Collapse
Affiliation(s)
- Colleen Fogarty Draper
- Nestle Institute of Health Sciences (NIHS), Lausanne, Switzerland.,Leiden University, Leiden, The Netherlands
| | | | | | - Cristiana Milone
- Independent Clinical Dietitian.,Canton Hospital of Luzern, Luzern, Switzerland
| | | | | | | | | | - MingMing Su
- University of Hawaii Cancer Center (UHCC), HI, USA
| | - Wei Jia
- University of Hawaii Cancer Center (UHCC), HI, USA
| | - Seu-Ping Guiraud
- Nestle Institute of Health Sciences (NIHS), Lausanne, Switzerland
| | | | | | | | | | - Nashmil Emami
- Clinical Development Unit, NRC, Lausanne, Switzerland
| | - Sofia Moco
- Nestle Institute of Health Sciences (NIHS), Lausanne, Switzerland
| | | | - Jim Kaput
- Nestle Institute of Health Sciences (NIHS), Lausanne, Switzerland
| | | |
Collapse
|
19
|
Grimaldi KA, van Ommen B, Ordovas JM, Parnell LD, Mathers JC, Bendik I, Brennan L, Celis-Morales C, Cirillo E, Daniel H, de Kok B, El-Sohemy A, Fairweather-Tait SJ, Fallaize R, Fenech M, Ferguson LR, Gibney ER, Gibney M, Gjelstad IMF, Kaput J, Karlsen AS, Kolossa S, Lovegrove J, Macready AL, Marsaux CFM, Alfredo Martinez J, Milagro F, Navas-Carretero S, Roche HM, Saris WHM, Traczyk I, van Kranen H, Verschuren L, Virgili F, Weber P, Bouwman J. Proposed guidelines to evaluate scientific validity and evidence for genotype-based dietary advice. Genes Nutr 2017; 12:35. [PMID: 29270237 PMCID: PMC5732517 DOI: 10.1186/s12263-017-0584-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 10/09/2017] [Indexed: 12/13/2022]
Abstract
Nutrigenetic research examines the effects of inter-individual differences in genotype on responses to nutrients and other food components, in the context of health and of nutrient requirements. A practical application of nutrigenetics is the use of personal genetic information to guide recommendations for dietary choices that are more efficacious at the individual or genetic subgroup level relative to generic dietary advice. Nutrigenetics is unregulated, with no defined standards, beyond some commercially adopted codes of practice. Only a few official nutrition-related professional bodies have embraced the subject, and, consequently, there is a lack of educational resources or guidance for implementation of the outcomes of nutrigenetic research. To avoid misuse and to protect the public, personalised nutrigenetic advice and information should be based on clear evidence of validity grounded in a careful and defensible interpretation of outcomes from nutrigenetic research studies. Evidence requirements are clearly stated and assessed within the context of state-of-the-art 'evidence-based nutrition'. We have developed and present here a draft framework that can be used to assess the strength of the evidence for scientific validity of nutrigenetic knowledge and whether 'actionable'. In addition, we propose that this framework be used as the basis for developing transparent and scientifically sound advice to the public based on nutrigenetic tests. We feel that although this area is still in its infancy, minimal guidelines are required. Though these guidelines are based on semi-quantitative data, they should stimulate debate on their utility. This framework will be revised biennially, as knowledge on the subject increases.
Collapse
Affiliation(s)
| | | | - Jose M. Ordovas
- JMUSDA-Human Nutrition Research Center on Aging at Tufts University, Boston, USA
- IMDEA Alimentacion, Madrid, Spain
| | - Laurence D. Parnell
- Agriculture Research Service, USDA, Human Nutrition Research Center on Aging, Boston, MA 02111 USA
| | - John C. Mathers
- Human Nutrition Research Centre, Institute of Cellular Medicine, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE4 5PL UK
| | - Igor Bendik
- DSM Nutritional Products, Kaiseraugst, Switzerland
| | - Lorraine Brennan
- UCD Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Republic of Ireland
| | - Carlos Celis-Morales
- Human Nutrition Research Centre, Institute of Cellular Medicine, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE4 5PL UK
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Science, University of Glasgow, Glasgow, G12 8TA UK
| | | | - Hannelore Daniel
- Nutritional Physiology, Technische Universität München, 85350 Freising, Germany
| | | | - Ahmed El-Sohemy
- Department of Nutritional Sciences, University of Toronto, 150 College Street, 3rd Floor, Toronto, ON M5S 3E2 Canada
| | | | - Rosalind Fallaize
- Hugh Sinclair Unit of Human Nutrition and Institute for Cardiovascular and Metabolic Research, Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, Berkshire RG6 6AP UK
| | - Michael Fenech
- CSIRO Health and Biosecurity, Gate 13, Kintore Avenue, Adelaide, SA 5000 Australia
| | - Lynnette R. Ferguson
- ACSRC and Discipline of Nutrition and Dietetics, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland, 1184 New Zealand
| | - Eileen R. Gibney
- UCD Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Republic of Ireland
| | - Mike Gibney
- UCD Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Republic of Ireland
| | - Ingrid M. F. Gjelstad
- Department of Nutrition, Universitetet i Oslo, PO Box 1046, Blindern, N-0316 Oslo, Norway
| | - Jim Kaput
- Vydiant Inc, 2330 Gold Meadow Way, Gold River, 95670 CA USA
| | - Anette S. Karlsen
- Department of Nutrition, Universitetet i Oslo, PO Box 1046, Blindern, N-0316 Oslo, Norway
| | - Silvia Kolossa
- Nutritional Physiology, Technische Universität München, 85350 Freising, Germany
| | - Julie Lovegrove
- Hugh Sinclair Unit of Human Nutrition and Institute for Cardiovascular and Metabolic Research, Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, Berkshire RG6 6AP UK
| | - Anna L. Macready
- Hugh Sinclair Unit of Human Nutrition and Institute for Cardiovascular and Metabolic Research, Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, Berkshire RG6 6AP UK
| | - Cyril F. M. Marsaux
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre + (MUMC+), Maastricht, The Netherlands
| | - J. Alfredo Martinez
- IMDEA Alimentacion, Madrid, Spain
- Department of Nutrition, Food Science and Physiology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain
- CIBERobn, Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Fermin Milagro
- Department of Nutrition, Food Science and Physiology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain
- CIBERobn, Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Santiago Navas-Carretero
- Department of Nutrition, Food Science and Physiology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain
- CIBERobn, Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Helen M. Roche
- Nutrigenomics Research Group, UCD Institute of Food and Health/UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Wim H. M. Saris
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre + (MUMC+), Maastricht, The Netherlands
| | - Iwona Traczyk
- Department of Human Nutrition, Faculty on Health Sciences, Medical University of Warsaw, Warsaw, Poland
| | - Henk van Kranen
- Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Faculty of Health, Medicine & Life Sciences, University of Maastricht, Universiteitssingel 40, 6229 ER Maastricht, The Netherlands
| | | | - Fabio Virgili
- Council for Agricultural Research and Economics, Food and Nutrition Research Centre, (CREA - AN), via Ardeatina 546, 00178 Rome, Italy
| | - Peter Weber
- DSM Nutritional Products, Kaiseraugst, Switzerland
| | | |
Collapse
|
20
|
Curran AM, Fogarty Draper C, Scott-Boyer MP, Valsesia A, Roche HM, Ryan MF, Gibney MJ, Kutmon M, Evelo CT, Coort SL, Astrup A, Saris WH, Brennan L, Kaput J. Sexual Dimorphism, Age, and Fat Mass Are Key Phenotypic Drivers of Proteomic Signatures. J Proteome Res 2017; 16:4122-4133. [DOI: 10.1021/acs.jproteome.7b00501] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Aoife M. Curran
- Institute
of Food and Health, Food for Health Ireland, University College Dublin, Dublin 4, Republic of Ireland
| | - Colleen Fogarty Draper
- Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
- Leiden
Academic Centre for Drug Research, Analytical BioSciences, Leiden University, 2311 EZ Leiden, The Netherlands
| | - Marie-Pier Scott-Boyer
- The Microsoft Research − University of Trento Centre for Computational and Systems Biology (COSBI), 38068 Rovereto, Italy
| | - Armand Valsesia
- Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Helen M. Roche
- Institute
of Food and Health, Food for Health Ireland, University College Dublin, Dublin 4, Republic of Ireland
- Nutrigenomics
Research Group, UCD Conway Institute of Biomolecular and Biomedical
Research and UCD Institute of Food and Health, School of Public Health,
Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin 4 Republic of Ireland
| | - Miriam F. Ryan
- Institute
of Food and Health, Food for Health Ireland, University College Dublin, Dublin 4, Republic of Ireland
| | - Michael J. Gibney
- Institute
of Food and Health, Food for Health Ireland, University College Dublin, Dublin 4, Republic of Ireland
| | - Martina Kutmon
- Department
of Bioinformatics − BiGCaT, School of Nutrition and Translational
Research in Metabolism and Maastricht
Centre for Systems Biology (McCSBio), Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Chris T. Evelo
- Department
of Bioinformatics − BiGCaT, School of Nutrition and Translational
Research in Metabolism and Maastricht
Centre for Systems Biology (McCSBio), Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Susan L. Coort
- Department
of Bioinformatics − BiGCaT, School of Nutrition and Translational
Research in Metabolism and Maastricht
Centre for Systems Biology (McCSBio), Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Arne Astrup
- Department
of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Wim H. Saris
- Department
of Human Biology, School of Nutrition and Translational Research in
Metabolism, Maastricht University Medical Centre, 6211 LK Maastricht, The Netherlands
| | - Lorraine Brennan
- Institute
of Food and Health, Food for Health Ireland, University College Dublin, Dublin 4, Republic of Ireland
| | - Jim Kaput
- Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| |
Collapse
|
21
|
Parolo S, Lacroix S, Kaput J, Scott-Boyer MP. Ancestors' dietary patterns and environments could drive positive selection in genes involved in micronutrient metabolism-the case of cofactor transporters. Genes Nutr 2017; 12:28. [PMID: 29043008 PMCID: PMC5628472 DOI: 10.1186/s12263-017-0579-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 09/19/2017] [Indexed: 02/06/2023]
Abstract
Background During evolution, humans colonized different ecological niches and adopted a variety of subsistence strategies that gave rise to diverse selective pressures acting across the genome. Environmentally induced selection of vitamin, mineral, or other cofactor transporters could influence micronutrient-requiring molecular reactions and contribute to inter-individual variability in response to foods and nutritional interventions. Methods A comprehensive list of genes coding for transporters of cofactors or their precursors was built using data mining procedures from the HGDP dataset and then explored to detect evidence of positive genetic selection. This dataset was chosen since it comprises several genetically diverse worldwide populations whom ancestries have evolved in different environments and thus lived following various nutritional habits and lifestyles. Results We identified 312 cofactor transporter (CT) genes involved in between-cell or sub-cellular compartment distribution of 28 cofactors derived from dietary intake. Twenty-four SNPs distributed across 14 CT genes separated populations into continental and intra-continental groups such as African hunter-gatherers and farmers, and between Native American sub-populations. Notably, four SNPs were located in SLC24A3 with one being a known eQTL of the NCKX3 protein. Conclusions These findings could support the importance of considering individual’s genetic makeup along with their metabolic profile when tailoring personalized dietary interventions for optimizing health. Electronic supplementary material The online version of this article (10.1186/s12263-017-0579-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Silvia Parolo
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), piazza Manifattura 1, 38068 Rovereto, TN Italy
| | - Sébastien Lacroix
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), piazza Manifattura 1, 38068 Rovereto, TN Italy
| | | | - Marie-Pier Scott-Boyer
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), piazza Manifattura 1, 38068 Rovereto, TN Italy
| |
Collapse
|
22
|
Kaput J, Perozzi G, Radonjic M, Virgili F. Propelling the paradigm shift from reductionism to systems nutrition. Genes Nutr 2017; 12:3. [PMID: 28138347 PMCID: PMC5264346 DOI: 10.1186/s12263-016-0549-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/13/2016] [Indexed: 12/14/2022]
Abstract
The complex physiology of living organisms represents a challenge for mechanistic understanding of the action of dietary bioactives in the human body and of their possible role in health and disease. Animal, cell, and microbial models have been extensively used to address questions that could not be pursued experimentally in humans, posing an additional level of complexity in translation of the results to healthy and diseased metabolism. The past few decades have witnessed a surge in development of increasingly sensitive molecular techniques and bioinformatic tools for storing, managing, and analyzing increasingly large datasets. Application of such powerful means to molecular nutrition research led to a major leap in study designs and experimental approaches yielding experimental data connecting dietary components to human health. Scientific journals bear major responsibilities in the advancement of science. As primary actors of dissemination to the scientific community, journals can impose rigid criteria for publishing only sound, reliable, and reproducible data. Journal policies are meant to guide potential authors to adopt the most updated standardization guidelines and shared best practices. Such policies evolve in parallel with the evolution of novel approaches and emerging challenges and therefore require constant updating. We highlight in this manuscript the major scientific issues that led to formulating new, updated journal policies for Genes & Nutrition, a journal which targets the growing field of nutritional systems biology interfacing personalized nutrition and preventive medicine, with the ultimate goal of promoting health and preventing or treating disease. We focus here on relevant issues requiring standardization in nutrition research. We also introduce new sections on human genetic variation and nutritional bioinformatics which follow the evolution of nutritional science into the twenty-first century.
Collapse
Affiliation(s)
- Jim Kaput
- Nestle Institute of Health Sciences, Lausanne, Switzerland
| | | | | | - Fabio Virgili
- CREA-NUT, Food & Nutrition Research Centre, Rome, Italy
| |
Collapse
|
23
|
Scott-Boyer MP, Lacroix S, Scotti M, Morine MJ, Kaput J, Priami C. A network analysis of cofactor-protein interactions for analyzing associations between human nutrition and diseases. Sci Rep 2016; 6:19633. [PMID: 26777674 PMCID: PMC4726080 DOI: 10.1038/srep19633] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 12/14/2015] [Indexed: 11/09/2022] Open
Abstract
The involvement of vitamins and other micronutrients in intermediary metabolism was elucidated in the mid 1900's at the level of individual biochemical reactions. Biochemical pathways remain the foundational knowledgebase for understanding how micronutrient adequacy modulates health in all life stages. Current daily recommended intakes were usually established on the basis of the association of a single nutrient to a single, most sensitive adverse effect and thus neglect interdependent and pleiotropic effects of micronutrients on biological systems. Hence, the understanding of the impact of overt or sub-clinical nutrient deficiencies on biological processes remains incomplete. Developing a more complete view of the role of micronutrients and their metabolic products in protein-mediated reactions is of importance. We thus integrated and represented cofactor-protein interaction data from multiple and diverse sources into a multi-layer network representation that links cofactors, cofactor-interacting proteins, biological processes, and diseases. Network representation of this information is a key feature of the present analysis and enables the integration of data from individual biochemical reactions and protein-protein interactions into a systems view, which may guide strategies for targeted nutritional interventions aimed at improving health and preventing diseases.
Collapse
Affiliation(s)
- Marie Pier Scott-Boyer
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Sébastien Lacroix
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Marco Scotti
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.,GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Melissa J Morine
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Jim Kaput
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Corrado Priami
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.,Department of Mathematics, University of Trento, Italy
| |
Collapse
|
24
|
Kaput J. Systems-Level Nutrition Approaches to Define Phenotypes Resulting from Complex Gene-Environment Interactions. Nestle Nutr Inst Workshop Ser 2016; 84:1-13. [PMID: 26764468 DOI: 10.1159/000436947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
High-throughput metabolomic, proteomic, and genomic technologies have delivered 21st-century data showing that humans cannot be randomized into groups: individuals are genetically and biochemically distinct. Gene-environment interactions caused by unique dietary and lifestyle factors contribute to the heterogeneity in physiologies observed in human studies. The risk factors determined for populations (i.e. the population-attributable risk) cannot be applied to the individual. Developing individual risk/benefit factors in light of the genetic diversity of human populations, the complexity of foods, culture and lifestyle, and the variety in metabolic processes that lead to health or disease are significant challenges for personalizing dietary advice for healthy or diseased individuals.
Collapse
|
25
|
Affiliation(s)
- Jim Kaput
- Nestlé Institute of Health Sciences, Lausanne, Switzerland,
| | | | | | | | | |
Collapse
|
26
|
Abstract
Healthy nutrition is accepted as a cornerstone of public health strategies for reducing the risk of noncommunicable conditions such as obesity, cardiovascular disease, and related morbidities. However, many research studies continue to focus on single or at most a few factors that may elicit a metabolic effect. These reductionist approaches resulted in: (1) exaggerated claims for nutrition as a cure or prevention of disease; (2) the wide use of empirically based dietary regimens, as if one fits all; and (3) frequent disappointment of consumers, patients, and healthcare providers about the real impact nutrition can make on medicine and health. Multiple factors including environment, host and microbiome genetics, social context, the chemical form of the nutrient, its (bio)availability, and chemical and metabolic interactions among nutrients all interact to result in nutrient requirement and in health outcomes. Advances in laboratory methodologies, especially in analytical and separation techniques, are making the chemical dissection of foods and their availability in physiological tissues possible in an unprecedented manner. These omics technologies have opened opportunities for extending knowledge of micronutrients and of their metabolic and endocrine roles. While these technologies are crucial, more holistic approaches to the analysis of physiology and environment, novel experimental designs, and more sophisticated computational methods are needed to advance our understanding of how nutrition influences health of individuals.
Collapse
Affiliation(s)
- Jacqueline Pontes Monteiro
- />Department of Pediatrics, Faculty of Medicine, Nutrition and Metabolism, University of São Paulo, Bandeirantes Avenue, HCFMRP Campus USP, 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Martin Kussmann
- />Nestlé Institute of Health Sciences, Innovation Square, EPFL Campus, 1015 Lausanne, Switzerland
- />Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland
| | - Jim Kaput
- />Nestlé Institute of Health Sciences, Innovation Square, EPFL Campus, 1015 Lausanne, Switzerland
- />Service d’endorcrinologie, diabetologie et metabolosime du CHUV, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
27
|
Varma V, Boros LG, Nolen GT, Chang CW, Wabitsch M, Beger RD, Kaput J. Metabolic fate of fructose in human adipocytes: a targeted 13C tracer fate association study. Metabolomics 2015; 11:529-544. [PMID: 25972768 PMCID: PMC4419153 DOI: 10.1007/s11306-014-0716-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 07/18/2014] [Indexed: 11/12/2022]
Abstract
The development of obesity is becoming an international problem and the role of fructose is unclear. Studies using liver tissue and hepatocytes have contributed to the understanding of fructose metabolism. Excess fructose consumption also affects extra hepatic tissues including adipose tissue. The effects of fructose on human adipocytes are not yet fully characterized, although in vivo studies have noted increased adiposity and weight gain in response to fructose sweetened-beverages. In order to understand and predict the metabolic responses of adipocytes to fructose, this study examined differentiating and differentiated human adipocytes in culture, exposed to a range of fructose concentrations equivalent to that reported in blood after consuming fructose. A stable isotope based dynamic profiling method using [U-13C6]-d-fructose tracer was used to examine the metabolism and fate of fructose. A targeted stable isotope tracer fate association method was used to analyze metabolic fluxes and flux surrogates with exposure to escalating fructose concentration. This study demonstrated that fructose stimulates anabolic processes in adipocytes robustly, including glutamate and de novo fatty acid synthesis. Furthermore, fructose also augments the release of free palmitate from fully differentiated adipocytes. These results imply that in the presence of fructose, the metabolic response of adipocytes in culture is altered in a dose dependent manner, particularly favoring increased glutamate and fatty acid synthesis and release, warranting further in vivo studies.
Collapse
Affiliation(s)
- Vijayalakshmi Varma
- Division of Systems Biology, National Center for Toxicological Research, FDA, 3900 NCTR Road, Jefferson, AR 72079 USA
| | - László G. Boros
- SiDMAP LLC, Los Angeles, CA 90064 USA
- Los Angeles Biomedical Research Institute (LABIOMED), Harbor-UCLA Medical Center, Torrance, CA 90502 USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Greg T. Nolen
- Division of Systems Biology, National Center for Toxicological Research, FDA, 3900 NCTR Road, Jefferson, AR 72079 USA
| | - Ching-Wei Chang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Jefferson, AR 72079 USA
| | - Martin Wabitsch
- Division of Pediatric Endocrinology and Diabetology, University of Ulm, Ulm, Germany
| | - Richard D. Beger
- Division of Systems Biology, National Center for Toxicological Research, FDA, 3900 NCTR Road, Jefferson, AR 72079 USA
| | - Jim Kaput
- Division of Systems Biology, National Center for Toxicological Research, FDA, 3900 NCTR Road, Jefferson, AR 72079 USA
- Systems Nutrition and Health, Nestle Institute of Health Sciences, Lausanne, Switzerland
| |
Collapse
|
28
|
Abstract
The term "Translational Genomics" reflects both title and mission of this new journal. "Translational" has traditionally been understood as "applied research" or "development", different from or even opposed to "basic research". Recent scientific and societal developments have triggered a re-assessment of the connotation that "translational" and "basic" are either/or activities: translational research nowadays aims at feeding the best science into applications and solutions for human society. We therefore argue here basic science to be challenged and leveraged for its relevance to human health and societal benefits. This more recent approach and attitude are catalyzed by four trends or developments: evidence-based solutions; large-scale, high dimensional data; consumer/patient empowerment; and systems-level understanding.
Collapse
Affiliation(s)
- Martin Kussmann
- Molecular Biomarkers Core, Nestlé Institute of Health Sciences (NIHS), Lausanne, Switzerland; Faculty of Life Sciences, Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne, Switzerland; Faculty of Science, Interdisciplinary NanoScience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Jim Kaput
- Systems Nutrition and Health Unit, Nestlé Institute of Health Sciences (NIHS), Lausanne, Switzerland; Service Endocrinol. Diabetes, Metabol. Univ. Hospital Lausanne (CHUV), Univ. Lausanne, Switzerland
| |
Collapse
|
29
|
Mitchell ES, Conus N, Kaput J. B vitamin polymorphisms and behavior: evidence of associations with neurodevelopment, depression, schizophrenia, bipolar disorder and cognitive decline. Neurosci Biobehav Rev 2014; 47:307-20. [PMID: 25173634 DOI: 10.1016/j.neubiorev.2014.08.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 07/11/2014] [Accepted: 08/18/2014] [Indexed: 11/16/2022]
Abstract
The B vitamins folic acid, vitamin B12 and B6 are essential for neuronal function, and severe deficiencies have been linked to increased risk of neurodevelopmental disorders, psychiatric disease and dementia. Polymorphisms of genes involved in B vitamin absorption, metabolism and function, such as methylene tetrahydrofolate reductase (MTHFR), cystathionine β synthase (CβS), transcobalamin 2 receptor (TCN2) and methionine synthase reductase (MTRR), have also been linked to increased incidence of psychiatric and cognitive disorders. However, the effects of these polymorphisms are often quite small and many studies failed to show any meaningful or consistent associations. This review discusses previous findings from clinical studies and highlights gaps in knowledge. Future studies assessing B vitamin-associated polymorphisms must take into account not just traditional demographics, but subjects' overall diet, relevant biomarkers of nutritional status and also analyze related genetic factors that may exacerbate behavioral effects or nutritional status.
Collapse
Affiliation(s)
- E Siobhan Mitchell
- Nestle Institute of Health Science, Innovation Park, EPFL Campus, Lausanne 1015, Switzerland.
| | - Nelly Conus
- Nestle Institute of Health Science, Innovation Park, EPFL Campus, Lausanne 1015, Switzerland
| | - Jim Kaput
- Nestle Institute of Health Science, Innovation Park, EPFL Campus, Lausanne 1015, Switzerland
| |
Collapse
|
30
|
Kaput J, Monteiro J, Morine M. Developing N of 1 translational research strategies. PharmaNutrition 2014. [DOI: 10.1016/j.phanu.2013.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
31
|
Morine MJ, Monteiro JP, Wise C, Teitel C, Pence L, Williams A, Ning B, McCabe-Sellers B, Champagne C, Turner J, Shelby B, Bogle M, Beger RD, Priami C, Kaput J. Genetic associations with micronutrient levels identified in immune and gastrointestinal networks. Genes Nutr 2014; 9:408. [PMID: 24879315 PMCID: PMC4169061 DOI: 10.1007/s12263-014-0408-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 05/12/2014] [Indexed: 01/05/2023]
Abstract
The discovery of vitamins and clarification of their role in preventing frank essential nutrient deficiencies occurred in the early 1900s. Much vitamin research has understandably focused on public health and the effects of single nutrients to alleviate acute conditions. The physiological processes for maintaining health, however, are complex systems that depend upon interactions between multiple nutrients, environmental factors, and genetic makeup. To analyze the relationship between these factors and nutritional health, data were obtained from an observational, community-based participatory research program of children and teens (age 6–14) enrolled in a summer day camp in the Delta region of Arkansas. Assessments of erythrocyte S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), plasma homocysteine (Hcy) and 6 organic micronutrients (retinol, 25-hydroxy vitamin D3, pyridoxal, thiamin, riboflavin, and vitamin E), and 1,129 plasma proteins were performed at 3 time points in each of 2 years. Genetic makeup was analyzed with 1 M SNP genotyping arrays, and nutrient status was assessed with 24-h dietary intake questionnaires. A pattern of metabolites (met_PC1) that included the ratio of erythrocyte SAM/SAH, Hcy, and 5 vitamins were identified by principal component analysis. Met_PC1 levels were significantly associated with (1) single-nucleotide polymorphisms, (2) levels of plasma proteins, and (3) multilocus genotypes coding for gastrointestinal and immune functions, as identified in a global network of metabolic/protein–protein interactions. Subsequent mining of data from curated pathway, network, and genome-wide association studies identified genetic and functional relationships that may be explained by gene–nutrient interactions. The systems nutrition strategy described here has thus associated a multivariate metabolite pattern in blood with genes involved in immune and gastrointestinal functions.
Collapse
Affiliation(s)
- Melissa J Morine
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Monteiro JP, Wise C, Morine MJ, Teitel C, Pence L, Williams A, McCabe-Sellers B, Champagne C, Turner J, Shelby B, Ning B, Oguntimein J, Taylor L, Toennessen T, Priami C, Beger RD, Bogle M, Kaput J. Methylation potential associated with diet, genotype, protein, and metabolite levels in the Delta Obesity Vitamin Study. Genes Nutr 2014; 9:403. [PMID: 24760553 PMCID: PMC4026438 DOI: 10.1007/s12263-014-0403-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 04/06/2014] [Indexed: 12/28/2022]
Abstract
Micronutrient research typically focuses on analyzing the effects of single or a few nutrients on health by analyzing a limited number of biomarkers. The observational study described here analyzed micronutrients, plasma proteins, dietary intakes, and genotype using a systems approach. Participants attended a community-based summer day program for 6-14 year old in 2 years. Genetic makeup, blood metabolite and protein levels, and dietary differences were measured in each individual. Twenty-four-hour dietary intakes, eight micronutrients (vitamins A, D, E, thiamin, folic acid, riboflavin, pyridoxal, and pyridoxine) and 3 one-carbon metabolites [homocysteine (Hcy), S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH)], and 1,129 plasma proteins were analyzed as a function of diet at metabolite level, plasma protein level, age, and sex. Cluster analysis identified two groups differing in SAM/SAH and differing in dietary intake patterns indicating that SAM/SAH was a potential marker of nutritional status. The approach used to analyze genetic association with the SAM/SAH metabolites is called middle-out: SNPs in 275 genes involved in the one-carbon pathway (folate, pyridoxal/pyridoxine, thiamin) or were correlated with SAM/SAH (vitamin A, E, Hcy) were analyzed instead of the entire 1M SNP data set. This procedure identified 46 SNPs in 25 genes associated with SAM/SAH demonstrating a genetic contribution to the methylation potential. Individual plasma metabolites correlated with 99 plasma proteins. Fourteen proteins correlated with body mass index, 49 with group age, and 30 with sex. The analytical strategy described here identified subgroups for targeted nutritional interventions.
Collapse
Affiliation(s)
- Jacqueline Pontes Monteiro
- />Department of Pediatrics, Faculty of Medicine, Faculty of Nutrition and Metabolism, University of São Paulo, Ribeirão Prêto, SP Brazil
| | - Carolyn Wise
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Melissa J. Morine
- />Department of Mathematics, University of Trento, Trento, Italy
- />The Microsoft Research, University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Candee Teitel
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Lisa Pence
- />Division of Systems Biology, NCTR/FDA, Jefferson, AR USA
| | - Anna Williams
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Beverly McCabe-Sellers
- />Delta Obesity Prevention Research Unit, United States Department of Agriculture, Agricultural Research Service, Little Rock, AR USA
| | - Catherine Champagne
- />Dietary Assessment and Nutrition Counseling, Pennington Biomedical Research Center, Baton Rouge, LA USA
| | - Jerome Turner
- />Boys, Girls, Adults Community Development Center & The Phillips County Community Partners, Marvell, AR USA
| | - Beatrice Shelby
- />Boys, Girls, Adults Community Development Center & The Phillips County Community Partners, Marvell, AR USA
| | - Baitang Ning
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Joan Oguntimein
- />Shepherd Program for the Interdisciplinary Study of Poverty and Human Capability, Washington and Lee University, Lexington, VA USA
- />Medical School, Drexel University, Philadelphia, PA USA
| | - Lauren Taylor
- />Shepherd Program for the Interdisciplinary Study of Poverty and Human Capability, Washington and Lee University, Lexington, VA USA
- />Emory School of Public Health, Atlanta, GA USA
| | - Terri Toennessen
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Corrado Priami
- />Department of Mathematics, University of Trento, Trento, Italy
- />The Microsoft Research, University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | | | - Margaret Bogle
- />Delta Obesity Prevention Research Unit, United States Department of Agriculture, Agricultural Research Service, Little Rock, AR USA
| | - Jim Kaput
- />Systems Nutrition and Health Unit, Nestle Institute of Health Sciences, Innovation Square, EPFL Campus, 1015 Lausanne, Switzerland
| |
Collapse
|
33
|
Kaput J, van Ommen B, Kremer B, Priami C, Monteiro JP, Morine M, Pepping F, Diaz Z, Fenech M, He Y, Albers R, Drevon CA, Evelo CT, Hancock REW, Ijsselmuiden C, Lumey LH, Minihane AM, Muller M, Murgia C, Radonjic M, Sobral B, West KP. Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life. Genes Nutr 2014; 9:378. [PMID: 24363221 PMCID: PMC3896628 DOI: 10.1007/s12263-013-0378-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/02/2013] [Indexed: 12/20/2022]
Abstract
Nutrition research, like most biomedical disciplines, adopted and often uses experimental approaches based on Beadle and Tatum's one gene-one polypeptide hypothesis, thereby reducing biological processes to single reactions or pathways. Systems thinking is needed to understand the complexity of health and disease processes requiring measurements of physiological processes, as well as environmental and social factors, which may alter the expression of genetic information. Analysis of physiological processes with omics technologies to assess systems' responses has only become available over the past decade and remains costly. Studies of environmental and social conditions known to alter health are often not connected to biomedical research. While these facts are widely accepted, developing and conducting comprehensive research programs for health are often beyond financial and human resources of single research groups. We propose a new research program on essential nutrients for optimal underpinning of growth and health (ENOUGH) that will use systems approaches with more comprehensive measurements and biostatistical analysis of the many biological and environmental factors that influence undernutrition. Creating a knowledge base for nutrition and health is a necessary first step toward developing solutions targeted to different populations in diverse social and physical environments for the two billion undernourished people in developed and developing economies.
Collapse
Affiliation(s)
- Jim Kaput
- Clinical Translation Unit, Nestle Institute of Health Sciences, Lausanne, Switzerland,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Abstract
We review here the status of human type 2 diabetes studies from a genetic, epidemiological, and clinical (intervention) perspective. Most studies limit analyses to one or a few omic technologies providing data of components of physiological processes. Since all chronic diseases are multifactorial and arise from complex interactions between genetic makeup and environment, type 2 diabetes mellitus (T2DM) is a collection of sub-phenotypes resulting in high fasting glucose. The underlying gene–environment interactions that produce these classes of T2DM are imperfectly characterized. Based on assessments of the complexity of T2DM, we propose a systems biology approach to advance the understanding of origin, onset, development, prevention, and treatment of this complex disease. This systems-based strategy is based on new study design principles and the integrated application of omics technologies: we pursue longitudinal studies in which each subject is analyzed at both homeostasis and after (healthy and safe) challenges. Each enrolled subject functions thereby as their own case and control and this design avoids assigning the subjects a priori to case and control groups based on limited phenotyping. Analyses at different time points along this longitudinal investigation are performed with a comprehensive set of omics platforms. These data sets are generated in a biological context, rather than biochemical compound class-driven manner, which we term “systems omics.”
Collapse
Affiliation(s)
- Martin Kussmann
- Nestlé Institute of Health Sciences SA Lausanne, Switzerland ; Faculty of Life Sciences, Ecole Polytechnique Fédérale Lausanne, Switzerland ; Faculty of Science, Aarhus University Aarhus, Denmark
| | | | | | | | | |
Collapse
|
35
|
Abstract
The progress in and success of biomedical research over the past century was built on the foundation outlined in R.A. Fisher's The Design of Experiments (1935), which described the theory and methodological approach to designing research studies. A key tenet of Fisher's treatise, widely adopted by the research community, is randomization, the process of assigning individuals to random groups or treatments. Comparing outcomes or responses between these groups yields “risk factors” called population attributable risks (PAR), which are statistical estimates of the percentage reduction in disease if the risk were avoided or in the case of genetic associations, if the gene variant were not present in the population .High throughput metabolomics, proteomic and genomic technologies provide 21st century data that humans cannot be randomized into groups: individuals are genetically and biochemically distinct. Gene–environment interactions caused by unique dietary and lifestyle factors contribute to heterogeneity in physiologies observed in human studies. The risk factors determined for populations (i.e., PAR) cannot be applied to the individual. Developing individual risk or benefit factors in light of the genetic diversity of human populations, the complexity of foods, culture and lifestyle, and the variety of metabolic processes that lead to health or disease are significant challenges for personalizing dietary advice for healthy or medical treatments for individuals with chronic disease.
Collapse
Affiliation(s)
- Jim Kaput
- Nestle Institute of Health Sciences, Lausanne, Switzerland.
| | | |
Collapse
|
36
|
Yang L, Price ET, Chang CW, Li Y, Huang Y, Guo LW, Guo Y, Kaput J, Shi L, Ning B. Gene expression variability in human hepatic drug metabolizing enzymes and transporters. PLoS One 2013; 8:e60368. [PMID: 23637747 PMCID: PMC3634068 DOI: 10.1371/journal.pone.0060368] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 02/26/2013] [Indexed: 12/17/2022] Open
Abstract
Interindividual variability in the expression of drug-metabolizing enzymes and transporters (DMETs) in human liver may contribute to interindividual differences in drug efficacy and adverse reactions. Published studies that analyzed variability in the expression of DMET genes were limited by sample sizes and the number of genes profiled. We systematically analyzed the expression of 374 DMETs from a microarray data set consisting of gene expression profiles derived from 427 human liver samples. The standard deviation of interindividual expression for DMET genes was much higher than that for non-DMET genes. The 20 DMET genes with the largest variability in the expression provided examples of the interindividual variation. Gene expression data were also analyzed using network analysis methods, which delineates the similarities of biological functionalities and regulation mechanisms for these highly variable DMET genes. Expression variability of human hepatic DMET genes may affect drug-gene interactions and disease susceptibility, with concomitant clinical implications.
Collapse
Affiliation(s)
- Lun Yang
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Elvin T. Price
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Ching-Wei Chang
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Yan Li
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Ying Huang
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California, United States of America
| | - Li-Wu Guo
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Yongli Guo
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Jim Kaput
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Leming Shi
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
- * E-mail: (BN); (LS)
| | - Baitang Ning
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
- * E-mail: (BN); (LS)
| |
Collapse
|
37
|
Patrinos GP, Smith TD, Howard H, Al-Mulla F, Chouchane L, Hadjisavvas A, Hamed SA, Li XT, Marafie M, Ramesar RS, Ramos FJ, de Ravel T, El-Ruby MO, Shrestha TR, Sobrido MJ, Tadmouri G, Witsch-Baumgartner M, Zilfalil BA, Auerbach AD, Carpenter K, Cutting GR, Dung VC, Grody W, Hasler J, Jorde L, Kaput J, Macek M, Matsubara Y, Padilla C, Robinson H, Rojas-Martinez A, Taylor GR, Vihinen M, Weber T, Burn J, Qi M, Cotton RGH, Rimoin D. Human Variome Project country nodes: documenting genetic information within a country. Hum Mutat 2012; 33:1513-9. [PMID: 22753370 DOI: 10.1002/humu.22147] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/04/2012] [Indexed: 11/09/2022]
Abstract
The Human Variome Project (http://www.humanvariomeproject.org) is an international effort aiming to systematically collect and share information on all human genetic variation. The two main pillars of this effort are gene/disease-specific databases and a network of Human Variome Project Country Nodes. The latter are nationwide efforts to document the genomic variation reported within a specific population. The development and successful operation of the Human Variome Project Country Nodes are of utmost importance to the success of Human Variome Project's aims and goals because they not only allow the genetic burden of disease to be quantified in different countries, but also provide diagnosticians and researchers access to an up-to-date resource that will assist them in their daily clinical practice and biomedical research, respectively. Here, we report the discussions and recommendations that resulted from the inaugural meeting of the International Confederation of Countries Advisory Council, held on 12th December 2011, during the 2011 Human Variome Project Beijing Meeting. We discuss the steps necessary to maximize the impact of the Country Node effort for developing regional and country-specific clinical genetics resources and summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects.
Collapse
Affiliation(s)
- George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Inselman AL, Hansen DK, Lee HY, Nakamura N, Ning B, Monteiro JP, Varma V, Kaput J. Assessment of research models for testing gene-environment interactions. Eur J Pharmacol 2011; 668 Suppl 1:S108-16. [PMID: 21816149 DOI: 10.1016/j.ejphar.2011.05.084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/16/2011] [Accepted: 05/22/2011] [Indexed: 12/16/2022]
Abstract
Throughout the last century, possible effects of exposure to toxicants, nutrients or drugs were examined primarily by studies of groups or populations. Individual variation in responses was acknowledged but could not be analyzed due to lack of information or tools to analyze individual genetic make-ups and lifestyle factors such as diet and activity. The Human Genome, Haplotype Map, 1000Genomes, and Human Variome Projects are identifying and cataloging the variation found within humans. Advances in DNA sequencing technologies will soon permit the characterization of individual genomes in clinical and basic research studies, thus allowing associations to be made between an individual genotype and the response to a particular exposure. Such knowledge and tools have generated a significant challenge for scientists: to design and conduct research studies that account for individual genetic variation. However, before these studies are done in humans, they will be performed in various in vivo and in vitro models. The advantages and disadvantages of some of the model test systems that are being used or developed in relation to individual genetic make-up and responses to xenobiotics are discussed.
Collapse
Affiliation(s)
- Amy L Inselman
- Division of Personalized Nutrition and Medicine, NCTR/FDA, 3900 NCTR Rd., Jefferson, AR 72079, United States.
| | | | | | | | | | | | | | | |
Collapse
|
39
|
AlAama J, Smith TD, Lo A, Howard H, Kline AA, Lange M, Kaput J, Cotton RG. Initiating a Human Variome Project Country Node. Hum Mutat 2011; 32:501-6. [DOI: 10.1002/humu.21463] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 01/24/2011] [Accepted: 01/25/2011] [Indexed: 11/06/2022]
|
40
|
Kohonen-Corish MRJ, Al-Aama JY, Auerbach AD, Axton M, Barash CI, Bernstein I, Béroud C, Burn J, Cunningham F, Cutting GR, den Dunnen JT, Greenblatt MS, Kaput J, Katz M, Lindblom A, Macrae F, Maglott D, Möslein G, Povey S, Ramesar R, Richards S, Seminara D, Sobrido MJ, Tavtigian S, Taylor G, Vihinen M, Winship I, Cotton RGH. How to catch all those mutations--the report of the third Human Variome Project Meeting, UNESCO Paris, May 2010. Hum Mutat 2011; 31:1374-81. [PMID: 20960468 DOI: 10.1002/humu.21379] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The third Human Variome Project (HVP) Meeting "Integration and Implementation" was held under UNESCO Patronage in Paris, France, at the UNESCO Headquarters May 10-14, 2010. The major aims of the HVP are the collection, curation, and distribution of all human genetic variation affecting health. The HVP has drawn together disparate groups, by country, gene of interest, and expertise, who are working for the common good with the shared goal of pushing the boundaries of the human variome and collaborating to avoid unnecessary duplication. The meeting addressed the 12 key areas that form the current framework of HVP activities: Ethics; Nomenclature and Standards; Publication, Credit and Incentives; Data Collection from Clinics; Overall Data Integration and Access-Peripheral Systems/Software; Data Collection from Laboratories; Assessment of Pathogenicity; Country Specific Collection; Translation to Healthcare and Personalized Medicine; Data Transfer, Databasing, and Curation; Overall Data Integration and Access-Central Systems; and Funding Mechanisms and Sustainability. In addition, three societies that support the goals and the mission of HVP also held their own Workshops with the view to advance disease-specific variation data collection and utilization: the International Society for Gastrointestinal Hereditary Tumours, the Micronutrient Genomics Project, and the Neurogenetics Consortium.
Collapse
Affiliation(s)
- Maija R J Kohonen-Corish
- Cancer Research Program, Garvan Institute of Medical Research, St. Vincent's Clinical School, University of NSW, Sydney, NSW, Australia.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Guo L, Dial S, Shi L, Branham W, Liu J, Fang JL, Green B, Deng H, Kaput J, Ning B. Similarities and differences in the expression of drug-metabolizing enzymes between human hepatic cell lines and primary human hepatocytes. Drug Metab Dispos 2011; 39:528-38. [PMID: 21149542 PMCID: PMC3061558 DOI: 10.1124/dmd.110.035873] [Citation(s) in RCA: 370] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Accepted: 12/13/2010] [Indexed: 01/08/2023] Open
Abstract
In addition to primary human hepatocytes, hepatoma cell lines, and transfected nonhepatoma, hepatic cell lines have been used for pharmacological and toxicological studies. However, a systematic evaluation and a general report of the gene expression spectra of drug-metabolizing enzymes and transporters (DMETs) in these in vitro systems are not currently available. To fill this information gap and to provide references for future studies, we systematically characterized the basal gene expression profiles of 251 drug-metabolizing enzymes in untreated primary human hepatocytes from six donors, four commonly used hepatoma cell lines (HepG2, Huh7, SK-Hep-1, and Hep3B), and one transfected human liver epithelial cell line. A large variation in DMET expression spectra was observed between hepatic cell lines and primary hepatocytes, with the complete absence or much lower abundance of certain DMETs in hepatic cell lines. Furthermore, the basal DMET expression spectra of five hepatic cell lines are summarized, providing references for researchers to choose carefully appropriate in vitro models for their studies of drug metabolism and toxicity, especially for studies with drugs in which toxicities are mediated through the formation of reactive metabolites.
Collapse
Affiliation(s)
- Lei Guo
- Division of Biochemical Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Varma V, Wise C, Kaput J. Carbohydrate metabolic pathway genes associated with quantitative trait loci (QTL) for obesity and type 2 diabetes: identification by data mining. Biotechnol J 2010; 5:942-9. [PMID: 20845384 DOI: 10.1002/biot.201000067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Increasing consumption of refined carbohydrates is now being recognized as a primary contributor to the development of nutritionally related chronic diseases such as obesity and type 2 diabetes mellitus (T2DM). A data mining approach was used to evaluate the role of carbohydrate metabolic pathway genes in the development of obesity and T2DM. Data from public databases were used to map the position of the carbohydrate metabolic pathway genes to known quantitative trait loci (QTL) for obesity and T2DM and for examining the pathway genes for the presence of sequence and structural genetic variants such as single nucleotide polymorphisms (SNPs) and copy number variants (CNS), respectively. The results demonstrated that a majority of the genes of the carbohydrate metabolic pathways are associated with QTL for obesity and many for T2DM. In addition, some key genes of the pathways also encode non-synonymous SNPs that exhibit significant differences in population frequencies. This study emphasizes the significance of the metabolic pathways genes in the development of disease phenotypes, its differential occurrence across populations and between individuals, and a strategy for interpreting an individuals' risk for disease.
Collapse
Affiliation(s)
- Vijayalakshmi Varma
- Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Jefferson, AR 72079, USA.
| | | | | |
Collapse
|
43
|
Kaput J, Evelo CT, Perozzi G, van Ommen B, Cotton R. Connecting the Human Variome Project to nutrigenomics. Genes Nutr 2010; 5:275-283. [PMID: 28300226 PMCID: PMC2989367 DOI: 10.1007/s12263-010-0186-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 09/24/2010] [Indexed: 10/19/2022]
Abstract
Nutrigenomics is the science of analyzing and understanding gene-nutrient interactions, which because of the genetic heterogeneity, varying degrees of interaction among gene products, and the environmental diversity is a complex science. Although much knowledge of human diversity has been accumulated, estimates suggest that ~90% of genetic variation has not yet been characterized. Identification of the DNA sequence variants that contribute to nutrition-related disease risk is essential for developing a better understanding of the complex causes of disease in humans, including nutrition-related disease. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) is an international effort to systematically identify genes, their mutations, and their variants associated with phenotypic variability and indications of human disease or phenotype. Since nutrigenomic research uses genetic information in the design and analysis of experiments, the HVP is an essential collaborator for ongoing studies of gene-nutrient interactions. With the advent of next generation sequencing methodologies and the understanding of the undiscovered variation in human genomes, the nutrigenomic community will be generating novel sequence data and results. The guidelines and practices of the HVP can guide and harmonize these efforts.
Collapse
Affiliation(s)
- Jim Kaput
- Division of Personalised Nutrition and Medicine, FDA/National Center for Toxicological Research, 3900 NCTR Road, Jefferson, AR 72079 USA
| | - Chris T. Evelo
- Department of Bioinformatics (BiGCaT), Maastricht University, Maastricht, The Netherlands
| | - Giuditta Perozzi
- INRAN—National Research Institute on Food & Nutrition, Via Ardeatina 546, 00178 Rome, Italy
| | - Ben van Ommen
- TNO Quality of Life, P.O. box 360, 3700 AJ Zeist, The Netherlands
| | - Richard Cotton
- Genomic Disorders Research Centre, Level 2, Alan Gilbert Building, 161 Barry Street, Melbourne, VIC 3053 Australia
| |
Collapse
|
44
|
Stumbo PJ, Weiss R, Newman JW, Pennington JA, Tucker KL, Wiesenfeld PL, Illner AK, Klurfeld DM, Kaput J. Web-enabled and improved software tools and data are needed to measure nutrient intakes and physical activity for personalized health research. J Nutr 2010; 140:2104-15. [PMID: 20980656 PMCID: PMC3139235 DOI: 10.3945/jn.110.128371] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 07/27/2010] [Accepted: 09/16/2010] [Indexed: 02/04/2023] Open
Abstract
Food intake, physical activity (PA), and genetic makeup each affect health and each factor influences the impact of the other 2 factors. Nutrigenomics describes interactions between genes and environment. Knowledge about the interplay between environment and genetics would be improved if experimental designs included measures of nutrient intake and PA. Lack of familiarity about how to analyze environmental variables and ease of access to tools and measurement instruments are 2 deterrents to these combined studies. This article describes the state of the art for measuring food intake and PA to encourage researchers to make their tools better known and more available to workers in other fields. Information presented was discussed during a workshop on this topic sponsored by the USDA, NIH, and FDA in the spring of 2009.
Collapse
Affiliation(s)
- Phyllis J Stumbo
- Institute for Clinical and Translational Science, University of Iowa, Iowa City, IA 52242, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
van Ommen B, El-Sohemy A, Hesketh J, Kaput J, Fenech M, Evelo CT, McArdle HJ, Bouwman J, Lietz G, Mathers JC, Fairweather-Tait S, van Kranen H, Elliott R, Wopereis S, Ferguson LR, Méplan C, Perozzi G, Allen L, Rivero D. The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research. Genes Nutr 2010; 5:285-96. [PMID: 21189865 PMCID: PMC2989004 DOI: 10.1007/s12263-010-0192-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Accepted: 10/13/2010] [Indexed: 01/19/2023]
Abstract
Micronutrients influence multiple metabolic pathways including oxidative and inflammatory processes. Optimum micronutrient supply is important for the maintenance of homeostasis in metabolism and, ultimately, for maintaining good health. With advances in systems biology and genomics technologies, it is becoming feasible to assess the activity of single and multiple micronutrients in their complete biological context. Existing research collects fragments of information, which are not stored systematically and are thus not optimally disseminated. The Micronutrient Genomics Project (MGP) was established as a community-driven project to facilitate the development of systematic capture, storage, management, analyses, and dissemination of data and knowledge generated by biological studies focused on micronutrient–genome interactions. Specifically, the MGP creates a public portal and open-source bioinformatics toolbox for all “omics” information and evaluation of micronutrient and health studies. The core of the project focuses on access to, and visualization of, genetic/genomic, transcriptomic, proteomic and metabolomic information related to micronutrients. For each micronutrient, an expert group is or will be established combining the various relevant areas (including genetics, nutrition, biochemistry, and epidemiology). Each expert group will (1) collect all available knowledge, (2) collaborate with bioinformatics teams towards constructing the pathways and biological networks, and (3) publish their findings on a regular basis. The project is coordinated in a transparent manner, regular meetings are organized and dissemination is arranged through tools, a toolbox web portal, a communications website and dedicated publications.
Collapse
Affiliation(s)
- Ben van Ommen
- TNO Quality of Life, P.O. box 360, 3700 AJ Zeist, The Netherlands
| | - Ahmed El-Sohemy
- Department of Nutritional Sciences, University of Toronto, 150 College Street, Toronto, ON M5S 3E2 Canada
| | - John Hesketh
- Institute for Cell and Molecular Biosciences, Newcastle University Medical School and Human Nutrition Research Centre, Newcastle-upon-Tyne, NE2 4HH UK
| | - Jim Kaput
- Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079 USA
| | - Michael Fenech
- CSIRO Food and Nutritional Sciences, PO Box 10041, Adelaide BC, SA 5000 Australia
| | - Chris T. Evelo
- Department of Bioinformatics—BiGCaT, Maastricht University, Maastricht, The Netherlands
| | - Harry J. McArdle
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, AB21 9SB UK
| | - Jildau Bouwman
- TNO Quality of Life, P.O. box 360, 3700 AJ Zeist, The Netherlands
| | - Georg Lietz
- Human Nutrition Research Centre, School of Agriculture, Food and Rural Development, Newcastle University, Kings Road, Agriculture Building, Newcastle upon Tyne, NE1 7RU UK
| | - John C. Mathers
- Human Nutrition Research Centre, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
| | - Sue Fairweather-Tait
- School of Medicine, Health Policy and Practice, University of East Anglia, Norwich, NR4 7TJ UK
| | | | - Ruan Elliott
- Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA UK
| | - Suzan Wopereis
- TNO Quality of Life, P.O. box 360, 3700 AJ Zeist, The Netherlands
| | - Lynnette R. Ferguson
- Discipline of Nutrition, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Catherine Méplan
- Institute for Cell and Molecular Biosciences, Newcastle University Medical School and Human Nutrition Research Centre, Newcastle-upon-Tyne, NE2 4HH UK
| | - Giuditta Perozzi
- Department of Nutritional Sciences—INRAN, National Research Institute on Food & Nutrition, Via Ardeatina 546, 00178 Rome, Italy
| | - Lindsay Allen
- USDA, ARS Western Human Nutrition Research Center, University of California, 530 W. Health Sciences Drive, Davis, CA 95616 USA
| | - Damariz Rivero
- Department of Pharmacology, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy
| | | |
Collapse
|
46
|
Abstract
Background Recent advances in high-throughput genotyping technology are paving the way for research in personalized medicine and nutrition. However, most of the genetic markers identified from association studies account for a small contribution to the total risk/benefit of the studied phenotypic trait. Testing whether the candidate genes identified by association studies are causal is critically important to the development of personalized medicine and nutrition. An efficient data mining strategy and a set of sophisticated tools are necessary to help better understand and utilize the findings from genetic association studies. Description SNP (single nucleotide polymorphism) and QTL (quantitative trait locus) libraries were constructed and incorporated into ArrayTrack, with user-friendly interfaces and powerful search features. Data from several public repositories were collected in the SNP and QTL libraries and connected to other domain libraries (genes, proteins, metabolites, and pathways) in ArrayTrack. Linking the data sets within ArrayTrack allows searching of SNP and QTL data as well as their relationships to other biological molecules. The SNP library includes approximately 15 million human SNPs and their annotations, while the QTL library contains publically available QTLs identified in mouse, rat, and human. The QTL library was developed for finding the overlap between the map position of a candidate or metabolic gene and QTLs from these species. Two use cases were included to demonstrate the utility of these tools. The SNP and QTL libraries are freely available to the public through ArrayTrack at http://www.fda.gov/ArrayTrack. Conclusions These libraries developed in ArrayTrack contain comprehensive information on SNPs and QTLs and are further cross-linked to other libraries. Connecting domain specific knowledge is a cornerstone of systems biology strategies and allows for a better understanding of the genetic and biological context of the findings from genetic association studies.
Collapse
Affiliation(s)
- Joshua Xu
- Z-Tech Corporation, ICF International company at NCTR, National Center for Toxicological Research, 3900 NCTR Rd, Jefferson, AR 72079, USA.
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Penn L, Boeing H, Boushey CJ, Dragsted LO, Kaput J, Scalbert A, Welch AA, Mathers JC. Assessment of dietary intake: NuGO symposium report. Genes Nutr 2010; 5:205-13. [PMID: 21052527 PMCID: PMC2935535 DOI: 10.1007/s12263-010-0175-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 04/13/2010] [Indexed: 11/26/2022]
Abstract
Advances in genomics science and associated bioinformatics and technology mean that excellent tools are available for characterising human genotypes. At the same time, approaches for characterising individual phenotypes are developing rapidly. In contrast, there has been much less investment in novel methodology for measuring dietary exposures so that there is now a significant gap in the toolkit for those investigating how diet interacts with genotype to determine phenotype. This symposium reviewed the strengths and limitations of current tools used in assessment of dietary intake and the potential to improve these tools through, for example, the use of statistical techniques that combine information from different sources (such as modelling and calibration methods) to ameliorate measurement error and to provide validity checks. Speakers examined the use of approaches based on technologies such as mobile ‘phones, digital cameras and Web-based systems which offer the potential for more acceptable (for study participants) and less laborious (for researchers and participants) routes to more robust data collection. In addition, the application of omics, especially metabolomics, tools to biofluids to identify new biomarkers of intake offers great potential to provide objective measures of food consumption with the advantage that data may be collected in forms that can be integrated readily with other high throughput (nutrigenomic) technologies.
Collapse
|
48
|
van Ommen B, Bouwman J, Dragsted LO, Drevon CA, Elliott R, de Groot P, Kaput J, Mathers JC, Müller M, Pepping F, Saito J, Scalbert A, Radonjic M, Rocca-Serra P, Travis A, Wopereis S, Evelo CT. Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies. Genes Nutr 2010; 5:189-203. [PMID: 21052526 PMCID: PMC2935528 DOI: 10.1007/s12263-010-0167-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 01/03/2010] [Indexed: 11/25/2022]
Abstract
The challenge of modern nutrition and health research is to identify food-based strategies promoting life-long optimal health and well-being. This research is complex because it exploits a multitude of bioactive compounds acting on an extensive network of interacting processes. Whereas nutrition research can profit enormously from the revolution in ‘omics’ technologies, it has discipline-specific requirements for analytical and bioinformatic procedures. In addition to measurements of the parameters of interest (measures of health), extensive description of the subjects of study and foods or diets consumed is central for describing the nutritional phenotype. We propose and pursue an infrastructural activity of constructing the “Nutritional Phenotype database” (dbNP). When fully developed, dbNP will be a research and collaboration tool and a publicly available data and knowledge repository. Creation and implementation of the dbNP will maximize benefits to the research community by enabling integration and interrogation of data from multiple studies, from different research groups, different countries and different—omics levels. The dbNP is designed to facilitate storage of biologically relevant, pre-processed—omics data, as well as study descriptive and study participant phenotype data. It is also important to enable the combination of this information at different levels (e.g. to facilitate linkage of data describing participant phenotype, genotype and food intake with information on study design and—omics measurements, and to combine all of this with existing knowledge). The biological information stored in the database (i.e. genetics, transcriptomics, proteomics, biomarkers, metabolomics, functional assays, food intake and food composition) is tailored to nutrition research and embedded in an environment of standard procedures and protocols, annotations, modular data-basing, networking and integrated bioinformatics. The dbNP is an evolving enterprise, which is only sustainable if it is accepted and adopted by the wider nutrition and health research community as an open source, pre-competitive and publicly available resource where many partners both can contribute and profit from its developments. We introduce the Nutrigenomics Organisation (NuGO, http://www.nugo.org) as a membership association responsible for establishing and curating the dbNP. Within NuGO, all efforts related to dbNP (i.e. usage, coordination, integration, facilitation and maintenance) will be directed towards a sustainable and federated infrastructure.
Collapse
Affiliation(s)
- Ben van Ommen
- TNO Quality of Life, PO Box 360, 6700 AJ Zeist, The Netherlands
| | - Jildau Bouwman
- TNO Quality of Life, PO Box 360, 6700 AJ Zeist, The Netherlands
| | - Lars O. Dragsted
- Institute of Human Nutrition, University of Copenhagen, 30 Rolighedsvej, 1958 Frederiksberg C, Denmark
| | - Christian A. Drevon
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ruan Elliott
- Institute of Food Research, Norwich Research Park, Norwich, Norfolk NR4 7UA UK
| | - Philip de Groot
- Nutrigenomics Consortium, TI Food and Nutrition, P.O. Box 557, 6700AN Wageningen, The Netherlands
- Division of Human Nutrition, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Jim Kaput
- Division of Personalized Nutrition and Medicine, Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR USA
| | - John C. Mathers
- Human Nutrition Research Centre, Institute for Ageing and Health, Newcastle University, William Leech Building, Framlington Place, Newcastle, NE44 6HE UK
| | - Michael Müller
- Nutrigenomics Consortium, TI Food and Nutrition, P.O. Box 557, 6700AN Wageningen, The Netherlands
- Division of Human Nutrition, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Fre Pepping
- Division of Human Nutrition, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Jahn Saito
- Department of Bioinformatics (BiGCaT) and Department of Knowledge Engineering (DKE), Maastricht University, Maastricht, The Netherlands
| | - Augustin Scalbert
- INRA, UMR 1019, Unite´ de Nutrition Humaine, Centre de Recherche de Clermont-Ferrand/Theix, 63122 Saint-Genes-Champanelle, France
| | | | | | - Anthony Travis
- The Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn Aberdeen, Scotland, AB21 9SB UK
| | - Suzan Wopereis
- TNO Quality of Life, PO Box 360, 6700 AJ Zeist, The Netherlands
| | - Chris T. Evelo
- Department of Bioinformatics (BiGCaT), Maastricht University, Maastricht, The Netherlands
| |
Collapse
|
49
|
McCabe-Sellers BJ, Chenard CA, Lovera D, Champagne CM, Bogle ML, Kaput J. Readiness of food composition databases and food component analysis systems for nutrigenomics. J Food Compost Anal 2009. [DOI: 10.1016/j.jfca.2009.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
50
|
van Ommen B, Keijer J, Heil SG, Kaput J. Challenging homeostasis to define biomarkers for nutrition related health. Mol Nutr Food Res 2009; 53:795-804. [DOI: 10.1002/mnfr.200800390] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|